From 7a70e9f594000f8403c24c461aab09edd60227c6 Mon Sep 17 00:00:00 2001 From: Ed2uiz <32622519+Ed2uiz@users.noreply.github.com> Date: Fri, 19 Jan 2024 23:16:58 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20drieslab?= =?UTF-8?q?/dbMatrix@7bd6987ec5cda1f0756f979c643a3f3901726234=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/operations.html | 6 +++--- pkgdown.yml | 2 +- search.json | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/articles/operations.html b/articles/operations.html index 67f5f8a..90e2aa7 100644 --- a/articles/operations.html +++ b/articles/operations.html @@ -78,7 +78,7 @@

Operations

-

2024-01-18

+

2024-01-19

Source: vignettes/operations.Rmd
operations.Rmd
@@ -333,7 +333,7 @@

dbDenseMatrix Operations # preview dense

-
## connection :  /tmp/RtmpLHTiE8/file199d543eb6e7.duckdb 
+
## connection :  /tmp/RtmpSfKRJg/file19552d19c515.duckdb 
 ## table name : 'dense_test'
 ## 50 x 50  matrix of class "dbDenseMatrix"
 ##                                                              
@@ -344,7 +344,7 @@ 
transpose
 dbMatrix::t(dense)

-
## connection :  /tmp/RtmpLHTiE8/file199d543eb6e7.duckdb 
+
## connection :  /tmp/RtmpSfKRJg/file19552d19c515.duckdb 
 ## table name : 'dense_test'
 ## 50 x 50  matrix of class "dbDenseMatrix"

 
## [[ Colnames 'row1', 'row2', 'row3' ... suppressing 44 ...'row48', 'row49', 'row50' ]]

diff --git a/pkgdown.yml b/pkgdown.yml
index 2818e7d..659acf9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,7 +5,7 @@ articles:
   arithmetic: arithmetic.html
   operations: operations.html
   overview: overview.html
-last_built: 2024-01-18T21:03Z
+last_built: 2024-01-19T23:16Z
 urls:
   reference: https://drieslab.github.io/dbMatrix/reference
   article: https://drieslab.github.io/dbMatrix/articles
diff --git a/search.json b/search.json
index 0cbd4a6..64a924b 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
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This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see .   Copyright (C)    This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"get-test-data","dir":"Articles","previous_headings":"","what":"Get test data","title":"Arithmetic","text":"test file dgCMatrixor compressed sparse column matrix representing single cell gene expression matrix. file data directory package. Let’s load .rds file preview object. file contains 634 rows 624 columns. rows represent gene names columns represent cell names. values integers represent number times gene detected cell. Like single-cell RNA-seq data, matrix sparse.","code":"dgc <- readRDS(\"../data/dgc.rds\")  dplyr::glimpse(dgc) #> Loading required package: Matrix #> Formal class 'dgCMatrix' [package \"Matrix\"] with 6 slots #>   ..@ i       : int [1:170625] 0 6 10 17 21 22 25 31 33 35 ... #>   ..@ p       : int [1:625] 0 227 510 758 980 1293 1631 1976 2223 2434 ... #>   ..@ Dim     : int [1:2] 634 624 #>   ..@ Dimnames:List of 2 #>   .. ..$ : chr [1:634] \"Gna12\" \"Ccnd2\" \"Btbd17\" \"Sox9\" ... #>   .. ..$ : chr [1:624] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" ... #>   ..@ x       : num [1:170625] 1 1 1 1 1 1 6 2 1 1 ... #>   ..@ factors : list()"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"create-a-dbmatrix-object","dir":"Articles","previous_headings":"","what":"Create a dbMatrix object","title":"Arithmetic","text":"Let’s create dbSparseMatrix object dgc object.","code":"# Note: by default the constructor creates a dbMatrix object in-memory dbsm <- createDBMatrix(value = dgc,                         db_path = \":temp:\",                         name = 'visium',                         class = \"dbSparseMatrix\",                        overwrite = TRUE)  # preview the object dbsm #> connection :  :temp:  #> table name : 'visium' #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                   #> Gna12         1 2 1 1 9 1 3 5 3 . #> Ccnd2         . 1 1 . . 1 . 1 1 . #> Btbd17        . 1 1 1 . . 2 . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 1 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 1 . . . . . . . . 1"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"scalar-arithmetic","dir":"Articles","previous_headings":"","what":"Scalar Arithmetic","title":"Arithmetic","text":"dbMatrix emulates scalar arithmetic Matrix package. Note: Addition subtraction non-zero addends dbSparseMatrix results dbDenseMatrix.","code":"dbsm + 1 #> densifying sparse matrix on disk...done #> connection :  :temp:  #> table name : 'visium' #> 634 x 624  matrix of class \"dbDenseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                  #>    1 2 3 2 3 4 2 #>    2 1 2 2 2 2 1 #>    3 1 2 2 1 1 1 #>  632 1 2 1 1 1 1 #>  633 1 1 1 2 1 1 #>  634 2 1 1 1 1 1  dbsm * 100 #> connection :  :temp:  #> table name : 'visium' #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                                       #> Gna12         100 200 100 100 900 100 300 500 300   . #> Ccnd2           . 100 100   .   . 100   . 100 100   . #> Btbd17          . 100 100 100   .   . 200   .   .   . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935         . 100   .   .   .   .   .   .   .   . #> 9630013A20Rik   .   .   .   .   .   .   .   .   .   . #> 2900040C04Rik 100   .   .   .   .   .   .   .   . 100"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"matrix-arithmetic","dir":"Articles","previous_headings":"","what":"Matrix Arithmetic","title":"Arithmetic","text":"dbMatrix also supports matrix arithmetic dbMatrix objects conformable.","code":"dbsm + dbsm #> connection :  :temp:  #> table name : 'visium' #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                     #> Gna12         2 4 2 2 18 2 6 10 6 . #> Ccnd2         . 2 2 .  . 2 .  2 2 . #> Btbd17        . 2 2 2  . . 4  . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 2 . .  . . .  . . . #> 9630013A20Rik . . . .  . . .  . . . #> 2900040C04Rik 2 . . .  . . .  . . 2"},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"hadamard-product","dir":"Articles","previous_headings":"Matrix Multiplication","what":"Hadamard product","title":"Arithmetic","text":"","code":"dbsm * dbsm #> connection :  :temp:  #> table name : 'visium' #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                     #> Gna12         1 4 1 1 81 1 9 25 9 . #> Ccnd2         . 1 1 .  . 1 .  1 1 . #> Btbd17        . 1 1 1  . . 4  . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 1 . .  . . .  . . . #> 9630013A20Rik . . . .  . . .  . . . #> 2900040C04Rik 1 . . .  . . .  . . 1"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"matrix-product","dir":"Articles","previous_headings":"Matrix Multiplication","what":"Matrix product","title":"Arithmetic","text":"TODO","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"shutdown","dir":"Articles","previous_headings":"","what":"Shutdown","title":"Arithmetic","text":"","code":"dbMatrix::dbDisconnect(dbsm, shutdown = TRUE)"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Arithmetic","text":"","code":"sessionInfo() #> R version 4.3.2 (2023-10-31) #> Platform: x86_64-pc-linux-gnu (64-bit) #> Running under: Ubuntu 22.04.3 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] Matrix_1.6-1.1      dbMatrix_0.0.0.9013 #>  #> loaded via a namespace (and not attached): #>  [1] jsonlite_1.8.8     dplyr_1.1.4        compiler_4.3.2     tidyselect_1.2.0   #>  [5] blob_1.2.4         stringr_1.5.1      jquerylib_0.1.4    systemfonts_1.0.5  #>  [9] textshaping_0.3.7  yaml_2.3.8         fastmap_1.1.1      lattice_0.21-9     #> [13] R6_2.5.1           generics_0.1.3     knitr_1.45         tibble_3.2.1       #> [17] desc_1.4.3         DBI_1.2.1          bslib_0.6.1        pillar_1.9.0       #> [21] rlang_1.1.3        utf8_1.2.4         cachem_1.0.8       stringi_1.8.3      #> [25] xfun_0.41          fs_1.6.3           sass_0.4.8         memoise_2.0.1      #> [29] cli_3.6.2          withr_3.0.0        pkgdown_2.0.7      magrittr_2.0.3     #> [33] grid_4.3.2         digest_0.6.34      dbplyr_2.4.0       lifecycle_1.0.4    #> [37] vctrs_0.6.5        evaluate_0.23      glue_1.7.0         data.table_1.14.10 #> [41] duckdb_0.9.2-1     ragg_1.2.7         fansi_1.0.6        rmarkdown_2.25     #> [45] purrr_1.0.2        tools_4.3.2        pkgconfig_2.0.3    htmltools_0.5.7"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Operations","text":"vignette introduces generic functions operations supported dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"loading-library","dir":"Articles","previous_headings":"","what":"Loading library","title":"Operations","text":"","code":"library(dbMatrix) library(Matrix)"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dbmatrix-generics","dir":"Articles","previous_headings":"","what":"dbMatrix generics","title":"Operations","text":"dbMatrix subclasses currently support basic generic functions listed support operations coming soon.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"get-test-data","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"Get test data","title":"Operations","text":"test file dgCMatrixor compressed sparse column matrix representing single cell gene expression matrix. file data directory package. Let’s load .rds file preview object.","code":"dgc <- readRDS(\"../data/dgc.rds\")  dplyr::glimpse(dgc) ## Formal class 'dgCMatrix' [package \"Matrix\"] with 6 slots ##   ..@ i       : int [1:170625] 0 6 10 17 21 22 25 31 33 35 ... ##   ..@ p       : int [1:625] 0 227 510 758 980 1293 1631 1976 2223 2434 ... ##   ..@ Dim     : int [1:2] 634 624 ##   ..@ Dimnames:List of 2 ##   .. ..$ : chr [1:634] \"Gna12\" \"Ccnd2\" \"Btbd17\" \"Sox9\" ... ##   .. ..$ : chr [1:624] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" ... ##   ..@ x       : num [1:170625] 1 1 1 1 1 1 6 2 1 1 ... ##   ..@ factors : list() # create dbSparseMatrix from the same dgc sparse = createDBMatrix(value = dgc,                          db_path = \":temp:\",                          name = \"sparse\",                          class = \"dbSparseMatrix\",                         overwrite = TRUE)  # preview  # show function aims to emulate the show method for dgCMatrix head(sparse) ## connection :  :temp:  ## table name : 'sparse' ## 6 x 624  matrix of class \"dbSparseMatrix\" ## [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] ##                              ## Gna12    . . . . . . . . . . ##  [ reached getOption(\"max.print\") -- omitted 5 rows ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"transpose","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"transpose","title":"Operations","text":"","code":"dbMatrix::t(sparse) ## connection :  :temp:  ## table name : 'sparse' ## 624 x 634  matrix of class \"dbSparseMatrix\" ## [[ Colnames 'Gna12', 'Ccnd2', 'Btbd17' ... suppressing 628 ...'Gm19935', '9630013A20Rik', '2900040C04Rik' ]] ##                                        ## AAAGGGATGTAGCAAG-1 1 . . . . . 1 . . . ##  [ reached getOption(\"max.print\") -- omitted 5 rows ] ## NA ##  ## ......suppressing 624 columns and 618 rows ##  ## NA ## NA ## NA"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colmeans","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"colMeans","title":"Operations","text":"","code":"dbMatrix::colMeans(sparse) ## AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1  ##          0.7413249          1.3296530          1.1435331          0.8343849  ## AACAACTGGTAGTTGC-1 AACAGGAAATCGAATA-1 AACAGGATGGGCCGCG-1 AACCATGGGATCGCTA-1  ##          1.6135647          2.2129338          1.7223975          1.9022082  ## AACCCAGAGACGGAGA-1 AACCGAGCTTGGTCAT-1  ##          0.7397476          0.9258675  ##  [ reached getOption(\"max.print\") -- omitted 614 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colsums","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"colSums","title":"Operations","text":"","code":"dbMatrix::colSums(sparse) ## AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1  ##                470                843                725                529  ## AACAACTGGTAGTTGC-1 AACAGGAAATCGAATA-1 AACAGGATGGGCCGCG-1 AACCATGGGATCGCTA-1  ##               1023               1403               1092               1206  ## AACCCAGAGACGGAGA-1 AACCGAGCTTGGTCAT-1  ##                469                587  ##  [ reached getOption(\"max.print\") -- omitted 614 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowmeans","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"rowMeans","title":"Operations","text":"","code":"dbMatrix::rowMeans(sparse) ##     Gna12     Ccnd2    Btbd17      Sox9      Sez6  Serpinf1    S100a6    Col1a1  ## 2.7179487 1.7323718 0.5528846 0.8766026 4.4679487 0.3092949 1.6522436 0.1185897  ##       Vwf      Esam  ## 0.6346154 0.4391026  ##  [ reached getOption(\"max.print\") -- omitted 624 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowsums","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"rowSums","title":"Operations","text":"","code":"dbMatrix::rowSums(sparse) ##    Gna12    Ccnd2   Btbd17     Sox9     Sez6 Serpinf1   S100a6   Col1a1  ##     1696     1081      345      547     2788      193     1031       74  ##      Vwf     Esam  ##      396      274  ##  [ reached getOption(\"max.print\") -- omitted 624 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dim","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"dim","title":"Operations","text":"","code":"dim(sparse) ## [1] 634 624 dim(dgc) ## [1] 634 624"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"check-results-are-equivalent","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"Check results are equivalent","title":"Operations","text":"","code":"all.equal(dbMatrix::colMeans(sparse), Matrix::colMeans(dgc)) ## [1] TRUE all.equal(dbMatrix::colSums(sparse), Matrix::colSums(dgc)) ## [1] TRUE all.equal(dbMatrix::rowMeans(sparse), Matrix::rowMeans(dgc)) ## [1] TRUE all.equal(dbMatrix::rowSums(sparse), Matrix::rowSums(dgc)) ## [1] TRUE"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dbdensematrix-operations","dir":"Articles","previous_headings":"","what":"dbDenseMatrix Operations","title":"Operations","text":"","code":"# below is a convenience function to simulate a dbDenseMatrix dense = dbMatrix::sim_dbDenseMatrix()  # preview dense ## connection :  /tmp/RtmpLHTiE8/file199d543eb6e7.duckdb  ## table name : 'dense_test' ## 50 x 50  matrix of class \"dbDenseMatrix\" ##                                                               ##   1  1.37096  0.321925  1.20097  0.216522  1.327505 -0.389880 ##  [ reached getOption(\"max.print\") -- omitted 5 rows ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"transpose-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"transpose","title":"Operations","text":"","code":"dbMatrix::t(dense) ## connection :  /tmp/RtmpLHTiE8/file199d543eb6e7.duckdb  ## table name : 'dense_test' ## 50 x 50  matrix of class \"dbDenseMatrix\" ## [[ Colnames 'row1', 'row2', 'row3' ... suppressing 44 ...'row48', 'row49', 'row50' ]] ##                                                               ##   1  1.37096 -0.564698  0.363128  1.444101 -0.431446  0.65565 ##  [ reached getOption(\"max.print\") -- omitted 5 rows ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colmeans-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"colMeans","title":"Operations","text":"","code":"dbMatrix::colMeans(dense) ##         col1         col2         col3         col4         col5         col6  ## -0.035671782  0.100701413 -0.151251089 -0.023716326  0.007939877 -0.028676220  ##         col7         col8         col9        col10  ## -0.061541347  0.127414276 -0.119421148 -0.116239863  ##  [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colsums-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"colSums","title":"Operations","text":"","code":"dbMatrix::colSums(dense) ##       col1       col2       col3       col4       col5       col6       col7  ## -1.7835891  5.0350707 -7.5625544 -1.1858163  0.3969938 -1.4338110 -3.0770674  ##       col8       col9      col10  ##  6.3707138 -5.9710574 -5.8119931  ##  [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowmeans-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"rowMeans","title":"Operations","text":"","code":"dbMatrix::rowMeans(dense) ##         row1         row2         row3         row4         row5         row6  ##  0.053643638  0.002494642  0.031334034  0.093889009 -0.048311439 -0.047287825  ##         row7         row8         row9        row10  ##  0.092209664 -0.023069981  0.096433464 -0.093495713  ##  [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowsums-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"rowSums","title":"Operations","text":"","code":"dbMatrix::rowSums(dense) ##       row1       row2       row3       row4       row5       row6       row7  ##  2.6821819  0.1247321  1.5667017  4.6944505 -2.4155720 -2.3643912  4.6104832  ##       row8       row9      row10  ## -1.1534990  4.8216732 -4.6747857  ##  [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"mean","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"mean","title":"Operations","text":"","code":"dbMatrix::mean(dense) ## [1] -0.009673541"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dim-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"dim","title":"Operations","text":"","code":"dim(dense) ## [1] 50 50"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"shutdown","dir":"Articles","previous_headings":"","what":"Shutdown","title":"Operations","text":"","code":"dbMatrix::dbDisconnect(dense, shutdown = TRUE)"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Operations","text":"","code":"sessionInfo() ## R version 4.3.2 (2023-10-31) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Ubuntu 22.04.3 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=C.UTF-8    LC_NUMERIC=C        LC_TIME=C.UTF-8     ##  [4] LC_COLLATE=C.UTF-8  LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 ##  [7] LC_PAPER=C.UTF-8    LC_NAME=C           LC_ADDRESS=C        ## [10] LC_TELEPHONE=C      ##  [ reached getOption(\"max.print\") -- omitted 2 entries ] ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] Matrix_1.6-1.1      dbMatrix_0.0.0.9013 ##  ## loaded via a namespace (and not attached): ##  [1] jsonlite_1.8.8    dplyr_1.1.4       compiler_4.3.2    tidyselect_1.2.0  ##  [5] blob_1.2.4        stringr_1.5.1     jquerylib_0.1.4   systemfonts_1.0.5 ##  [9] textshaping_0.3.7 yaml_2.3.8        ##  [ reached getOption(\"max.print\") -- omitted 38 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbmatrix","dir":"Articles","previous_headings":"","what":"dbMatrix","title":"Overview","text":"dbMatrix core package dbverse library inherits dbData base class consists two subclasses, dbSparseMatrix dbDenseMatrix. dbMatrix objects emulate -memory dense sparse matrices embedded database powered DuckDB.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbsparsematrix","dir":"Articles","previous_headings":"","what":"dbSparseMatrix","title":"Overview","text":"Sparse matrices represented triplet vectors , j, x numerical vectors. j refer row column indices, respectively, specific x values counts. Note: j vectors one-based following conventions Matrix R package TSparseMatrix class. dbSparseMatrix class stores triplet vector representation associated dimension names dimensions available. none provided, automatically generated factors (enums) row# col# labels rownames colnames, respectively. dbSparseMatrix class contain zeros triplet vector representation. Zero values inferred based provided dimensions. Support compressed sparse column matrices dgCMatrix class Matrix R package currently implemented. information sparse matrices, see wiki article .","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbdensematrix","dir":"Articles","previous_headings":"","what":"dbDenseMatrix","title":"Overview","text":"use approach dbSparseMatrix represent dense matrix triplet , j, x vector. difference dbDenseMatrix class consists values matrix, including zeros.","code":""},{"path":"https://drieslab.github.io/dbMatrix/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Edward C. Ruiz. Author. Jiaji George Chen. Author. Ruben Dries. Author, maintainer.","code":""},{"path":"https://drieslab.github.io/dbMatrix/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"C. Ruiz E, George Chen J, Dries R (2024). dbMatrix: dbMatrix. R package version 0.0.0.9013, https://drieslab.github.io/dbMatrix/.","code":"@Manual{,   title = {dbMatrix: dbMatrix},   author = {Edward {C. Ruiz} and Jiaji {George Chen} and Ruben Dries},   year = {2024},   note = {R package version 0.0.0.9013},   url = {https://drieslab.github.io/dbMatrix/}, }"},{"path":"https://drieslab.github.io/dbMatrix/index.html","id":"dbmatrix","dir":"","previous_headings":"","what":"dbMatrix","title":"dbMatrix","text":"dbMatrix core package dbverse library. goal dbMatrix support larger--memory matrix computations.","code":""},{"path":"https://drieslab.github.io/dbMatrix/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"dbMatrix","text":"can install development version dbMatrix Github like :","code":"# install.packages(\"pak\", repos = sprintf(\"https://r-lib.github.io/p/pak/stable/%s/%s/%s\", .Platform$pkgType, R.Version()$os, R.Version()$arch)) pak::pak(\"drieslab/dbMatrix\")"},{"path":"https://drieslab.github.io/dbMatrix/reference/DBI.html","id":null,"dir":"Reference","previous_headings":"","what":"dbDisconnect — dbDisconnect,dbMatrix-method","title":"dbDisconnect — dbDisconnect,dbMatrix-method","text":"dbDisconnect dbListTables","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/DBI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dbDisconnect — dbDisconnect,dbMatrix-method","text":"","code":"# S4 method for dbMatrix dbDisconnect(x, ...)  # S4 method for dbMatrix dbListTables(x, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/castNumeric.html","id":null,"dir":"Reference","previous_headings":"","what":"Set a column to numeric — castNumeric","title":"Set a column to numeric — castNumeric","text":"Sets column numeric first checking column data type. nothing column already double precaution avoid truncation values.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/castNumeric.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set a column to numeric — castNumeric","text":"","code":"# S4 method for dbData,character castNumeric(x, col, ...)  # S4 method for dbMatrix,missing castNumeric(x, col, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/castNumeric.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set a column to numeric — castNumeric","text":"x dbData data object col column cast numeric ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/colTypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Column data types of dbData objects — colTypes","title":"Column data types of dbData objects — colTypes","text":"Get column data types objects inherit 'dbData'","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/colTypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Column data types of dbData objects — colTypes","text":"","code":"# S4 method for dbData colTypes(x, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/colTypes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Column data types of dbData objects — colTypes","text":"x dbData data object ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a sparse or dense dbMatrix object — createDBMatrix","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"Create S4 dbMatrix object sparse dense triplet vector format.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"","code":"createDBMatrix(   value,   class = NULL,   db_path = \":temp:\",   overwrite = FALSE,   name = \"dbMatrix\",   dims = NULL,   dim_names = NULL,   ... )"},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"value data added database. See details supported data types (required) class class dbMatrix: dbDenseMatrix dbSparseMatrix (required) db_path path database disk (relative absolute) memory (\":temp:\") overwrite whether overwrite table already exists database (required) name table name assign within database (optional, default: \"dbMatrix\") dims dimensions matrix (optional: [int, int]) dim_names dimension names matrix (optional: list(enum, enum)) ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"function reads data pre-existing DuckDB database. Based name db_path lazy connection made downstream dbMatrix initialization. Supported value data types: dgCMatrix -memory sparse matrix Matrix package matrix -memory dense matrix base R .mtx Path .mtx file (TODO) .csv Path .csv file (TODO) tbl_duckdb_connection Table DuckDB database ijx format  existing dbMatrix object. dims dim_names must  specified value tbl_duckdb_connection.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"","code":"dgc <- dbMatrix:::sim_dgc() #> Error in as(data, \"dgCMatrix\"): no method or default for coercing “matrix” to “dgCMatrix” dbSparse <- createDBMatrix(value = dgc, db_path = \":temp:\",                            name = \"sparse_matrix\", class = \"dbSparseMatrix\",                            overwrite = TRUE) #> Error in eval(expr, envir, enclos): object 'dgc' not found dbSparse #> Error in eval(expr, envir, enclos): object 'dbSparse' not found"},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDataFrame-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 dbDataFrame class — dbDataFrame-class","title":"S4 dbDataFrame class — dbDataFrame-class","text":"Representation dataframes using -disk database. object used connection single table exists within database.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDataFrame-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 dbDataFrame class — dbDataFrame-class","text":"data dplyr tbl represents database data hash unique hash ID backend remote_name name table within database contains data key column set key ordering subsetting ","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDenseMatrix-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 Class for dbDenseMatrix — dbDenseMatrix-class","title":"S4 Class for dbDenseMatrix — dbDenseMatrix-class","text":"Representation dense matrices using -disk database. Inherits dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDenseMatrix-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 Class for dbDenseMatrix — dbDenseMatrix-class","text":"data dense ijx dataframe/tibble","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 dbMatrix class — dbMatrix-class","title":"S4 dbMatrix class — dbMatrix-class","text":"Representation sparse matrices using -disk database. object used connection single table exists within database.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 dbMatrix class — dbMatrix-class","text":"dim_names row [1] col [2] names dims dimensions matrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbSparseMatrix-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 Class for dbSparseMatrix — dbSparseMatrix-class","title":"S4 Class for dbSparseMatrix — dbSparseMatrix-class","text":"Representation sparse matrices using -disk database. Inherits dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/flex_window_order.html","id":null,"dir":"Reference","previous_headings":"","what":"flex_window_order — flex_window_order","title":"flex_window_order — flex_window_order","text":"workaround multiple dbplyr window column ordering","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/flex_window_order.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"flex_window_order — flex_window_order","text":"","code":"flex_window_order(x, order_cols)"},{"path":"https://drieslab.github.io/dbMatrix/reference/flex_window_order.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"flex_window_order — flex_window_order","text":"x dbplyr::tbl_lazy order_cols character vector column names","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":null,"dir":"Reference","previous_headings":"","what":"get_con — get_con","title":"get_con — get_con","text":"get_con","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_con — get_con","text":"","code":"get_con(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_con — get_con","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":null,"dir":"Reference","previous_headings":"","what":"get_dbdir — get_dbdir","title":"get_dbdir — get_dbdir","text":"get_dbdir","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_dbdir — get_dbdir","text":"","code":"get_dbdir(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_dbdir — get_dbdir","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":null,"dir":"Reference","previous_headings":"","what":"get_tblName — get_tblName","title":"get_tblName — get_tblName","text":"get_tblName","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_tblName — get_tblName","text":"","code":"get_tblName(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_tblName — get_tblName","text":"dbData","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbDataFrame-method.html","id":null,"dir":"Reference","previous_headings":"","what":"head — head,dbDataFrame-method","title":"head — head,dbDataFrame-method","text":"head","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbDataFrame-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"head — head,dbDataFrame-method","text":"","code":"# S4 method for dbDataFrame head(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"head — head,dbMatrix-method","title":"head — head,dbMatrix-method","text":"head","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"head — head,dbMatrix-method","text":"","code":"# S4 method for dbMatrix head(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/hidden_aliases.html","id":null,"dir":"Reference","previous_headings":"","what":"rowSums — [,dbData,missing,missing,missing-method","title":"rowSums — [,dbData,missing,missing,missing-method","text":"rowSums rowSums colSums colSums rowMeans rowMeans colMeans colMeans colSds colSds rowSds rowSds mean mean Transpose nrow ncol ncol ncol dim","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/hidden_aliases.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rowSums — [,dbData,missing,missing,missing-method","text":"","code":"# S4 method for dbData,missing,missing,missing [(x, i, j)  # S4 method for dbData,missing,missing,ANY [(x, i, j) <- value  # S4 method for dbMatrix,dbIndex,missing,missing [(x, i, j, ..., drop = TRUE)  # S4 method for dbMatrix,missing,dbIndex,missing [(x, i, j, ..., drop = TRUE)  # S4 method for dbMatrix,dbIndex,dbIndex,missing [(x, i, j, ..., drop = TRUE)  # S4 method for dbDataFrame,dbIndex,missing,ANY [(x, i, j, ..., drop = TRUE)  # S4 method for dbDataFrame,missing,dbIndex,ANY [(x, i, j, ..., drop = TRUE)  # S4 method for dbDataFrame,dbIndex,dbIndex,ANY [(x, i, j, ..., drop = FALSE)  # S4 method for dbDataFrame,missing,missing,missing [(x, i, j)  # S4 method for dbDataFrame,missing,missing,ANY [(x, i, j) <- value  # S4 method for dbDataFrame names(x)  # S4 method for dbDataFrame,dbIndex names(x) <- value  # S4 method for dbData rownames(x)  # S4 method for dbMatrix rownames(x)  # S4 method for dbMatrix rownames(x) <- value  # S4 method for dbData colnames(x)  # S4 method for dbMatrix colnames(x)  # S4 method for dbMatrix,ANY colnames(x) <- value  # S4 method for dbDataFrame,dbIndex colnames(x) <- value  # S4 method for dbMatrix dimnames(x)  # S4 method for dbMatrix,list dimnames(x) <- value  # S4 method for dbDataFrame dimnames(x)  # S4 method for dbDataFrame,list dimnames(x) <- value  # S4 method for dbMatrix,ANY Arith(e1, e2)  # S4 method for ANY,dbMatrix Arith(e1, e2)  # S4 method for dbMatrix,dbMatrix Arith(e1, e2)  # S4 method for dbMatrix,ANY Ops(e1, e2)  # S4 method for ANY,dbMatrix Ops(e1, e2)  # S4 method for dbMatrix,dbMatrix Ops(e1, e2)  # S4 method for dbDenseMatrix rowSums(x, ...)  # S4 method for dbSparseMatrix rowSums(x, ...)  # S4 method for dbDenseMatrix colSums(x, ...)  # S4 method for dbSparseMatrix colSums(x, ...)  # S4 method for dbDenseMatrix rowMeans(x, ...)  # S4 method for dbSparseMatrix rowMeans(x, ...)  # S4 method for dbDenseMatrix colMeans(x, ...)  # S4 method for dbSparseMatrix colMeans(x, ...)  # S4 method for dbDenseMatrix colSds(x, ...)  # S4 method for dbSparseMatrix colSds(x, ...)  # S4 method for dbDenseMatrix rowSds(x, ...)  # S4 method for dbSparseMatrix rowSds(x, ...)  # S4 method for dbDenseMatrix mean(x, ...)  # S4 method for dbSparseMatrix mean(x, ...)  # S4 method for dbMatrix t(x)  # S4 method for dbDataFrame nrow(x)  # S4 method for dbMatrix ncol(x)  # S4 method for dbDataFrame ncol(x)  # S4 method for dbDataFrame ncol(x)  # S4 method for dbMatrix dim(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow.html","id":null,"dir":"Reference","previous_headings":"","what":"The number of rows/cols — nrow","title":"The number of rows/cols — nrow","text":"nrow ncol return number rows columns present x.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The number of rows/cols — nrow","text":"","code":"# S4 method for dbMatrix nrow(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate array for pretty printing of matrix values — print_array","title":"Generate array for pretty printing of matrix values — print_array","text":"Generate array pretty printing matrix values","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate array for pretty printing of matrix values — print_array","text":"","code":"print_array(   i = NULL,   j = NULL,   x = NULL,   dims,   rownames = rep(\"\", dims[1]),   fill = \".\",   digits = 5L )"},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate array for pretty printing of matrix values — print_array","text":", j, x matched vectors integers j, value x dims dimensions array (integer vector 2) fill fill character digits default = 5. numeric, round number digits","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":null,"dir":"Reference","previous_headings":"","what":"sim_dgc — sim_duckdb","title":"sim_dgc — sim_duckdb","text":"Simulate dbSparseMatrix memory Simulate dbDenseMatrix memory.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"sim_dgc — sim_duckdb","text":"","code":"sim_duckdb(value = datasets::iris, name = \"test\", con = NULL, memory = TRUE)  sim_dgc(num_rows = 50, num_cols = 50, n_vals = 50)  sim_denseMat(num_rows = 50, num_cols = 50)  sim_ijx_matrix(mat_type = NULL, num_rows = 50, num_cols = 50, seed_num = 42)  sim_dbDataFrame(value = NULL, name = \"df_test\", key = NA_character_)  sim_dbSparseMatrix(   num_rows = 50,   num_cols = 50,   seed_num = 42,   name = \"sparse_test\",   memory = FALSE )  sim_dbDenseMatrix(   num_rows = 50,   num_cols = 50,   seed_num = 42,   name = \"dense_test\",   memory = FALSE )"},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"sim_dgc — sim_duckdb","text":"num_rows number rows matrix (default: 50) num_cols number columns matrix (default: 50) seed_num seed number reproducibility (default: 42)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"sim_dgc — sim_duckdb","text":"dgCMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"sim_dgc — sim_duckdb","text":"function generates simulated sparse matrix (dgCMatrix) number rows columns sets n_vals random values non-zero value. function generates simulated dense matrix object specified number rows columns. function generates ijx representation simulated dgCMatrix object specified number rows columns sets 50 random values non-zero value.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"sim_dgc — sim_duckdb","text":"sim_duckdb(): Simulate duckdb connection dplyr tbl_Pool memory sim_dgc(): Simulate dgcMatrix sim_denseMat(): Simulate dense matrix sim_ijx_matrix(): Simulate duckdb connection dplyr tbl_Pool memory sim_dbDataFrame(): Simulate dbDataFrame memory sim_dbSparseMatrix(): Simulate dbSparseMatrix memory sim_dbDenseMatrix(): Simulate dbDenseMatrix memory","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"sim_dgc — sim_duckdb","text":"","code":"sim_ijx_matrix() #> Error in sim_ijx_matrix(): could not find function \"sim_ijx_matrix\""},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbDataFrame-method.html","id":null,"dir":"Reference","previous_headings":"","what":"tail — tail,dbDataFrame-method","title":"tail — tail,dbDataFrame-method","text":"tail","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbDataFrame-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tail — tail,dbDataFrame-method","text":"","code":"# S4 method for dbDataFrame tail(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"tail — tail,dbMatrix-method","title":"tail — tail,dbMatrix-method","text":"tail","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tail — tail,dbMatrix-method","text":"","code":"# S4 method for dbMatrix tail(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"Convert dbSparseMatrix dbDenseMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"","code":"toDbDense(db_sparse)"},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"db_sparse dbSparseMatrix object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"","code":"TODO #> Error in eval(expr, envir, enclos): object 'TODO' not found"},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":null,"dir":"Reference","previous_headings":"","what":"to_ijx_disk — to_ijx_disk","title":"to_ijx_disk — to_ijx_disk","text":"to_ijx_disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"to_ijx_disk — to_ijx_disk","text":"","code":"to_ijx_disk(con, name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"to_ijx_disk — to_ijx_disk","text":"con duckdb connection name name table convert ijx disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"to_ijx_disk — to_ijx_disk","text":"remote table long format unpivoted wide format matrix","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Rename update dbIndex superclass fix indexing bugs.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Add experimental as_matrix() convenience function.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Update docs. Migrate site link drieslab. Move {Matrix} Imports.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"documentation-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Documentation","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Update overview.Rmd. 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Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C)     This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see .   Copyright (C)    This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"get-test-data","dir":"Articles","previous_headings":"","what":"Get test data","title":"Arithmetic","text":"test file dgCMatrixor compressed sparse column matrix representing single cell gene expression matrix. file data directory package. Let’s load .rds file preview object. file contains 634 rows 624 columns. rows represent gene names columns represent cell names. values integers represent number times gene detected cell. Like single-cell RNA-seq data, matrix sparse.","code":"dgc <- readRDS(\"../data/dgc.rds\")  dplyr::glimpse(dgc) #> Loading required package: Matrix #> Formal class 'dgCMatrix' [package \"Matrix\"] with 6 slots #>   ..@ i       : int [1:170625] 0 6 10 17 21 22 25 31 33 35 ... #>   ..@ p       : int [1:625] 0 227 510 758 980 1293 1631 1976 2223 2434 ... #>   ..@ Dim     : int [1:2] 634 624 #>   ..@ Dimnames:List of 2 #>   .. ..$ : chr [1:634] \"Gna12\" \"Ccnd2\" \"Btbd17\" \"Sox9\" ... #>   .. ..$ : chr [1:624] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" ... #>   ..@ x       : num [1:170625] 1 1 1 1 1 1 6 2 1 1 ... #>   ..@ factors : list()"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"create-a-dbmatrix-object","dir":"Articles","previous_headings":"","what":"Create a dbMatrix object","title":"Arithmetic","text":"Let’s create dbSparseMatrix object dgc object.","code":"# Note: by default the constructor creates a dbMatrix object in-memory dbsm <- createDBMatrix(value = dgc,                         db_path = \":temp:\",                         name = 'visium',                         class = \"dbSparseMatrix\",                        overwrite = TRUE)  # preview the object dbsm #> connection :  :temp:  #> table name : 'visium' #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                   #> Gna12         1 2 1 1 9 1 3 5 3 . #> Ccnd2         . 1 1 . . 1 . 1 1 . #> Btbd17        . 1 1 1 . . 2 . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 1 . . . . . . . . #> 9630013A20Rik . . . . . . . . . . #> 2900040C04Rik 1 . . . . . . . . 1"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"scalar-arithmetic","dir":"Articles","previous_headings":"","what":"Scalar Arithmetic","title":"Arithmetic","text":"dbMatrix emulates scalar arithmetic Matrix package. Note: Addition subtraction non-zero addends dbSparseMatrix results dbDenseMatrix.","code":"dbsm + 1 #> densifying sparse matrix on disk...done #> connection :  :temp:  #> table name : 'visium' #> 634 x 624  matrix of class \"dbDenseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                  #>    1 2 3 2 3 4 2 #>    2 1 2 2 2 2 1 #>    3 1 2 2 1 1 1 #>  632 1 2 1 1 1 1 #>  633 1 1 1 2 1 1 #>  634 2 1 1 1 1 1  dbsm * 100 #> connection :  :temp:  #> table name : 'visium' #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                                       #> Gna12         100 200 100 100 900 100 300 500 300   . #> Ccnd2           . 100 100   .   . 100   . 100 100   . #> Btbd17          . 100 100 100   .   . 200   .   .   . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935         . 100   .   .   .   .   .   .   .   . #> 9630013A20Rik   .   .   .   .   .   .   .   .   .   . #> 2900040C04Rik 100   .   .   .   .   .   .   .   . 100"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"matrix-arithmetic","dir":"Articles","previous_headings":"","what":"Matrix Arithmetic","title":"Arithmetic","text":"dbMatrix also supports matrix arithmetic dbMatrix objects conformable.","code":"dbsm + dbsm #> connection :  :temp:  #> table name : 'visium' #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                     #> Gna12         2 4 2 2 18 2 6 10 6 . #> Ccnd2         . 2 2 .  . 2 .  2 2 . #> Btbd17        . 2 2 2  . . 4  . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 2 . .  . . .  . . . #> 9630013A20Rik . . . .  . . .  . . . #> 2900040C04Rik 2 . . .  . . .  . . 2"},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"hadamard-product","dir":"Articles","previous_headings":"Matrix Multiplication","what":"Hadamard product","title":"Arithmetic","text":"","code":"dbsm * dbsm #> connection :  :temp:  #> table name : 'visium' #> 634 x 624  matrix of class \"dbSparseMatrix\" #> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] #>                                     #> Gna12         1 4 1 1 81 1 9 25 9 . #> Ccnd2         . 1 1 .  . 1 .  1 1 . #> Btbd17        . 1 1 1  . . 4  . . . #>  #> ......suppressing 614 columns and 628 rows #>  #> Gm19935       . 1 . .  . . .  . . . #> 9630013A20Rik . . . .  . . .  . . . #> 2900040C04Rik 1 . . .  . . .  . . 1"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"matrix-product","dir":"Articles","previous_headings":"Matrix Multiplication","what":"Matrix product","title":"Arithmetic","text":"TODO","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"shutdown","dir":"Articles","previous_headings":"","what":"Shutdown","title":"Arithmetic","text":"","code":"dbMatrix::dbDisconnect(dbsm, shutdown = TRUE)"},{"path":"https://drieslab.github.io/dbMatrix/articles/arithmetic.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Arithmetic","text":"","code":"sessionInfo() #> R version 4.3.2 (2023-10-31) #> Platform: x86_64-pc-linux-gnu (64-bit) #> Running under: Ubuntu 22.04.3 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] Matrix_1.6-1.1      dbMatrix_0.0.0.9013 #>  #> loaded via a namespace (and not attached): #>  [1] jsonlite_1.8.8     dplyr_1.1.4        compiler_4.3.2     tidyselect_1.2.0   #>  [5] blob_1.2.4         stringr_1.5.1      jquerylib_0.1.4    systemfonts_1.0.5  #>  [9] textshaping_0.3.7  yaml_2.3.8         fastmap_1.1.1      lattice_0.21-9     #> [13] R6_2.5.1           generics_0.1.3     knitr_1.45         tibble_3.2.1       #> [17] desc_1.4.3         DBI_1.2.1          bslib_0.6.1        pillar_1.9.0       #> [21] rlang_1.1.3        utf8_1.2.4         cachem_1.0.8       stringi_1.8.3      #> [25] xfun_0.41          fs_1.6.3           sass_0.4.8         memoise_2.0.1      #> [29] cli_3.6.2          withr_3.0.0        pkgdown_2.0.7      magrittr_2.0.3     #> [33] grid_4.3.2         digest_0.6.34      dbplyr_2.4.0       lifecycle_1.0.4    #> [37] vctrs_0.6.5        evaluate_0.23      glue_1.7.0         data.table_1.14.10 #> [41] duckdb_0.9.2-1     ragg_1.2.7         fansi_1.0.6        rmarkdown_2.25     #> [45] purrr_1.0.2        tools_4.3.2        pkgconfig_2.0.3    htmltools_0.5.7"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Operations","text":"vignette introduces generic functions operations supported dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"loading-library","dir":"Articles","previous_headings":"","what":"Loading library","title":"Operations","text":"","code":"library(dbMatrix) library(Matrix)"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dbmatrix-generics","dir":"Articles","previous_headings":"","what":"dbMatrix generics","title":"Operations","text":"dbMatrix subclasses currently support basic generic functions listed support operations coming soon.","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"get-test-data","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"Get test data","title":"Operations","text":"test file dgCMatrixor compressed sparse column matrix representing single cell gene expression matrix. file data directory package. Let’s load .rds file preview object.","code":"dgc <- readRDS(\"../data/dgc.rds\")  dplyr::glimpse(dgc) ## Formal class 'dgCMatrix' [package \"Matrix\"] with 6 slots ##   ..@ i       : int [1:170625] 0 6 10 17 21 22 25 31 33 35 ... ##   ..@ p       : int [1:625] 0 227 510 758 980 1293 1631 1976 2223 2434 ... ##   ..@ Dim     : int [1:2] 634 624 ##   ..@ Dimnames:List of 2 ##   .. ..$ : chr [1:634] \"Gna12\" \"Ccnd2\" \"Btbd17\" \"Sox9\" ... ##   .. ..$ : chr [1:624] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" ... ##   ..@ x       : num [1:170625] 1 1 1 1 1 1 6 2 1 1 ... ##   ..@ factors : list() # create dbSparseMatrix from the same dgc sparse = createDBMatrix(value = dgc,                          db_path = \":temp:\",                          name = \"sparse\",                          class = \"dbSparseMatrix\",                         overwrite = TRUE)  # preview  # show function aims to emulate the show method for dgCMatrix head(sparse) ## connection :  :temp:  ## table name : 'sparse' ## 6 x 624  matrix of class \"dbSparseMatrix\" ## [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]] ##                              ## Gna12    . . . . . . . . . . ##  [ reached getOption(\"max.print\") -- omitted 5 rows ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"transpose","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"transpose","title":"Operations","text":"","code":"dbMatrix::t(sparse) ## connection :  :temp:  ## table name : 'sparse' ## 624 x 634  matrix of class \"dbSparseMatrix\" ## [[ Colnames 'Gna12', 'Ccnd2', 'Btbd17' ... suppressing 628 ...'Gm19935', '9630013A20Rik', '2900040C04Rik' ]] ##                                        ## AAAGGGATGTAGCAAG-1 1 . . . . . 1 . . . ##  [ reached getOption(\"max.print\") -- omitted 5 rows ] ## NA ##  ## ......suppressing 624 columns and 618 rows ##  ## NA ## NA ## NA"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colmeans","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"colMeans","title":"Operations","text":"","code":"dbMatrix::colMeans(sparse) ## AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1  ##          0.7413249          1.3296530          1.1435331          0.8343849  ## AACAACTGGTAGTTGC-1 AACAGGAAATCGAATA-1 AACAGGATGGGCCGCG-1 AACCATGGGATCGCTA-1  ##          1.6135647          2.2129338          1.7223975          1.9022082  ## AACCCAGAGACGGAGA-1 AACCGAGCTTGGTCAT-1  ##          0.7397476          0.9258675  ##  [ reached getOption(\"max.print\") -- omitted 614 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colsums","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"colSums","title":"Operations","text":"","code":"dbMatrix::colSums(sparse) ## AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1  ##                470                843                725                529  ## AACAACTGGTAGTTGC-1 AACAGGAAATCGAATA-1 AACAGGATGGGCCGCG-1 AACCATGGGATCGCTA-1  ##               1023               1403               1092               1206  ## AACCCAGAGACGGAGA-1 AACCGAGCTTGGTCAT-1  ##                469                587  ##  [ reached getOption(\"max.print\") -- omitted 614 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowmeans","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"rowMeans","title":"Operations","text":"","code":"dbMatrix::rowMeans(sparse) ##     Gna12     Ccnd2    Btbd17      Sox9      Sez6  Serpinf1    S100a6    Col1a1  ## 2.7179487 1.7323718 0.5528846 0.8766026 4.4679487 0.3092949 1.6522436 0.1185897  ##       Vwf      Esam  ## 0.6346154 0.4391026  ##  [ reached getOption(\"max.print\") -- omitted 624 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowsums","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"rowSums","title":"Operations","text":"","code":"dbMatrix::rowSums(sparse) ##    Gna12    Ccnd2   Btbd17     Sox9     Sez6 Serpinf1   S100a6   Col1a1  ##     1696     1081      345      547     2788      193     1031       74  ##      Vwf     Esam  ##      396      274  ##  [ reached getOption(\"max.print\") -- omitted 624 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dim","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"dim","title":"Operations","text":"","code":"dim(sparse) ## [1] 634 624 dim(dgc) ## [1] 634 624"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"check-results-are-equivalent","dir":"Articles","previous_headings":"dbSparse Matrix Operations","what":"Check results are equivalent","title":"Operations","text":"","code":"all.equal(dbMatrix::colMeans(sparse), Matrix::colMeans(dgc)) ## [1] TRUE all.equal(dbMatrix::colSums(sparse), Matrix::colSums(dgc)) ## [1] TRUE all.equal(dbMatrix::rowMeans(sparse), Matrix::rowMeans(dgc)) ## [1] TRUE all.equal(dbMatrix::rowSums(sparse), Matrix::rowSums(dgc)) ## [1] TRUE"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dbdensematrix-operations","dir":"Articles","previous_headings":"","what":"dbDenseMatrix Operations","title":"Operations","text":"","code":"# below is a convenience function to simulate a dbDenseMatrix dense = dbMatrix::sim_dbDenseMatrix()  # preview dense ## connection :  /tmp/RtmpSfKRJg/file19552d19c515.duckdb  ## table name : 'dense_test' ## 50 x 50  matrix of class \"dbDenseMatrix\" ##                                                               ##   1  1.37096  0.321925  1.20097  0.216522  1.327505 -0.389880 ##  [ reached getOption(\"max.print\") -- omitted 5 rows ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"transpose-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"transpose","title":"Operations","text":"","code":"dbMatrix::t(dense) ## connection :  /tmp/RtmpSfKRJg/file19552d19c515.duckdb  ## table name : 'dense_test' ## 50 x 50  matrix of class \"dbDenseMatrix\" ## [[ Colnames 'row1', 'row2', 'row3' ... suppressing 44 ...'row48', 'row49', 'row50' ]] ##                                                               ##   1  1.37096 -0.564698  0.363128  1.444101 -0.431446  0.65565 ##  [ reached getOption(\"max.print\") -- omitted 5 rows ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colmeans-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"colMeans","title":"Operations","text":"","code":"dbMatrix::colMeans(dense) ##         col1         col2         col3         col4         col5         col6  ## -0.035671782  0.100701413 -0.151251089 -0.023716326  0.007939877 -0.028676220  ##         col7         col8         col9        col10  ## -0.061541347  0.127414276 -0.119421148 -0.116239863  ##  [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"colsums-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"colSums","title":"Operations","text":"","code":"dbMatrix::colSums(dense) ##       col1       col2       col3       col4       col5       col6       col7  ## -1.7835891  5.0350707 -7.5625544 -1.1858163  0.3969938 -1.4338110 -3.0770674  ##       col8       col9      col10  ##  6.3707138 -5.9710574 -5.8119931  ##  [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowmeans-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"rowMeans","title":"Operations","text":"","code":"dbMatrix::rowMeans(dense) ##         row1         row2         row3         row4         row5         row6  ##  0.053643638  0.002494642  0.031334034  0.093889009 -0.048311439 -0.047287825  ##         row7         row8         row9        row10  ##  0.092209664 -0.023069981  0.096433464 -0.093495713  ##  [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"rowsums-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"rowSums","title":"Operations","text":"","code":"dbMatrix::rowSums(dense) ##       row1       row2       row3       row4       row5       row6       row7  ##  2.6821819  0.1247321  1.5667017  4.6944505 -2.4155720 -2.3643912  4.6104832  ##       row8       row9      row10  ## -1.1534990  4.8216732 -4.6747857  ##  [ reached getOption(\"max.print\") -- omitted 40 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"mean","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"mean","title":"Operations","text":"","code":"dbMatrix::mean(dense) ## [1] -0.009673541"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"dim-1","dir":"Articles","previous_headings":"dbDenseMatrix Operations","what":"dim","title":"Operations","text":"","code":"dim(dense) ## [1] 50 50"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"shutdown","dir":"Articles","previous_headings":"","what":"Shutdown","title":"Operations","text":"","code":"dbMatrix::dbDisconnect(dense, shutdown = TRUE)"},{"path":"https://drieslab.github.io/dbMatrix/articles/operations.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Operations","text":"","code":"sessionInfo() ## R version 4.3.2 (2023-10-31) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Ubuntu 22.04.3 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=C.UTF-8    LC_NUMERIC=C        LC_TIME=C.UTF-8     ##  [4] LC_COLLATE=C.UTF-8  LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 ##  [7] LC_PAPER=C.UTF-8    LC_NAME=C           LC_ADDRESS=C        ## [10] LC_TELEPHONE=C      ##  [ reached getOption(\"max.print\") -- omitted 2 entries ] ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] Matrix_1.6-1.1      dbMatrix_0.0.0.9013 ##  ## loaded via a namespace (and not attached): ##  [1] jsonlite_1.8.8    dplyr_1.1.4       compiler_4.3.2    tidyselect_1.2.0  ##  [5] blob_1.2.4        stringr_1.5.1     jquerylib_0.1.4   systemfonts_1.0.5 ##  [9] textshaping_0.3.7 yaml_2.3.8        ##  [ reached getOption(\"max.print\") -- omitted 38 entries ]"},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbmatrix","dir":"Articles","previous_headings":"","what":"dbMatrix","title":"Overview","text":"dbMatrix core package dbverse library inherits dbData base class consists two subclasses, dbSparseMatrix dbDenseMatrix. dbMatrix objects emulate -memory dense sparse matrices embedded database powered DuckDB.","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbsparsematrix","dir":"Articles","previous_headings":"","what":"dbSparseMatrix","title":"Overview","text":"Sparse matrices represented triplet vectors , j, x numerical vectors. j refer row column indices, respectively, specific x values counts. Note: j vectors one-based following conventions Matrix R package TSparseMatrix class. dbSparseMatrix class stores triplet vector representation associated dimension names dimensions available. none provided, automatically generated factors (enums) row# col# labels rownames colnames, respectively. dbSparseMatrix class contain zeros triplet vector representation. Zero values inferred based provided dimensions. Support compressed sparse column matrices dgCMatrix class Matrix R package currently implemented. information sparse matrices, see wiki article .","code":""},{"path":"https://drieslab.github.io/dbMatrix/articles/overview.html","id":"dbdensematrix","dir":"Articles","previous_headings":"","what":"dbDenseMatrix","title":"Overview","text":"use approach dbSparseMatrix represent dense matrix triplet , j, x vector. difference dbDenseMatrix class consists values matrix, including zeros.","code":""},{"path":"https://drieslab.github.io/dbMatrix/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Edward C. Ruiz. Author. Jiaji George Chen. Author. Ruben Dries. Author, maintainer.","code":""},{"path":"https://drieslab.github.io/dbMatrix/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"C. Ruiz E, George Chen J, Dries R (2024). dbMatrix: dbMatrix. R package version 0.0.0.9013, https://drieslab.github.io/dbMatrix/.","code":"@Manual{,   title = {dbMatrix: dbMatrix},   author = {Edward {C. Ruiz} and Jiaji {George Chen} and Ruben Dries},   year = {2024},   note = {R package version 0.0.0.9013},   url = {https://drieslab.github.io/dbMatrix/}, }"},{"path":"https://drieslab.github.io/dbMatrix/index.html","id":"dbmatrix","dir":"","previous_headings":"","what":"dbMatrix","title":"dbMatrix","text":"dbMatrix core package dbverse library. goal dbMatrix support larger--memory matrix computations.","code":""},{"path":"https://drieslab.github.io/dbMatrix/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"dbMatrix","text":"can install development version dbMatrix Github like :","code":"# install.packages(\"pak\", repos = sprintf(\"https://r-lib.github.io/p/pak/stable/%s/%s/%s\", .Platform$pkgType, R.Version()$os, R.Version()$arch)) pak::pak(\"drieslab/dbMatrix\")"},{"path":"https://drieslab.github.io/dbMatrix/reference/DBI.html","id":null,"dir":"Reference","previous_headings":"","what":"dbDisconnect — dbDisconnect,dbMatrix-method","title":"dbDisconnect — dbDisconnect,dbMatrix-method","text":"dbDisconnect dbListTables","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/DBI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"dbDisconnect — dbDisconnect,dbMatrix-method","text":"","code":"# S4 method for dbMatrix dbDisconnect(x, ...)  # S4 method for dbMatrix dbListTables(x, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/castNumeric.html","id":null,"dir":"Reference","previous_headings":"","what":"Set a column to numeric — castNumeric","title":"Set a column to numeric — castNumeric","text":"Sets column numeric first checking column data type. nothing column already double precaution avoid truncation values.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/castNumeric.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set a column to numeric — castNumeric","text":"","code":"# S4 method for dbData,character castNumeric(x, col, ...)  # S4 method for dbMatrix,missing castNumeric(x, col, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/castNumeric.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set a column to numeric — castNumeric","text":"x dbData data object col column cast numeric ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/colTypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Column data types of dbData objects — colTypes","title":"Column data types of dbData objects — colTypes","text":"Get column data types objects inherit 'dbData'","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/colTypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Column data types of dbData objects — colTypes","text":"","code":"# S4 method for dbData colTypes(x, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/colTypes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Column data types of dbData objects — colTypes","text":"x dbData data object ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a sparse or dense dbMatrix object — createDBMatrix","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"Create S4 dbMatrix object sparse dense triplet vector format.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"","code":"createDBMatrix(   value,   class = NULL,   db_path = \":temp:\",   overwrite = FALSE,   name = \"dbMatrix\",   dims = NULL,   dim_names = NULL,   ... )"},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"value data added database. See details supported data types (required) class class dbMatrix: dbDenseMatrix dbSparseMatrix (required) db_path path database disk (relative absolute) memory (\":temp:\") overwrite whether overwrite table already exists database (required) name table name assign within database (optional, default: \"dbMatrix\") dims dimensions matrix (optional: [int, int]) dim_names dimension names matrix (optional: list(enum, enum)) ... additional params pass","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"function reads data pre-existing DuckDB database. Based name db_path lazy connection made downstream dbMatrix initialization. Supported value data types: dgCMatrix -memory sparse matrix Matrix package matrix -memory dense matrix base R .mtx Path .mtx file (TODO) .csv Path .csv file (TODO) tbl_duckdb_connection Table DuckDB database ijx format  existing dbMatrix object. dims dim_names must  specified value tbl_duckdb_connection.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/createDBMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a sparse or dense dbMatrix object — createDBMatrix","text":"","code":"dgc <- dbMatrix:::sim_dgc() #> Error in as(data, \"dgCMatrix\"): no method or default for coercing “matrix” to “dgCMatrix” dbSparse <- createDBMatrix(value = dgc, db_path = \":temp:\",                            name = \"sparse_matrix\", class = \"dbSparseMatrix\",                            overwrite = TRUE) #> Error in eval(expr, envir, enclos): object 'dgc' not found dbSparse #> Error in eval(expr, envir, enclos): object 'dbSparse' not found"},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDataFrame-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 dbDataFrame class — dbDataFrame-class","title":"S4 dbDataFrame class — dbDataFrame-class","text":"Representation dataframes using -disk database. object used connection single table exists within database.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDataFrame-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 dbDataFrame class — dbDataFrame-class","text":"data dplyr tbl represents database data hash unique hash ID backend remote_name name table within database contains data key column set key ordering subsetting ","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDenseMatrix-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 Class for dbDenseMatrix — dbDenseMatrix-class","title":"S4 Class for dbDenseMatrix — dbDenseMatrix-class","text":"Representation dense matrices using -disk database. Inherits dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbDenseMatrix-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 Class for dbDenseMatrix — dbDenseMatrix-class","text":"data dense ijx dataframe/tibble","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 dbMatrix class — dbMatrix-class","title":"S4 dbMatrix class — dbMatrix-class","text":"Representation sparse matrices using -disk database. object used connection single table exists within database.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbMatrix-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 dbMatrix class — dbMatrix-class","text":"dim_names row [1] col [2] names dims dimensions matrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/dbSparseMatrix-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 Class for dbSparseMatrix — dbSparseMatrix-class","title":"S4 Class for dbSparseMatrix — dbSparseMatrix-class","text":"Representation sparse matrices using -disk database. Inherits dbMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/flex_window_order.html","id":null,"dir":"Reference","previous_headings":"","what":"flex_window_order — flex_window_order","title":"flex_window_order — flex_window_order","text":"workaround multiple dbplyr window column ordering","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/flex_window_order.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"flex_window_order — flex_window_order","text":"","code":"flex_window_order(x, order_cols)"},{"path":"https://drieslab.github.io/dbMatrix/reference/flex_window_order.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"flex_window_order — flex_window_order","text":"x dbplyr::tbl_lazy order_cols character vector column names","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":null,"dir":"Reference","previous_headings":"","what":"get_con — get_con","title":"get_con — get_con","text":"get_con","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_con — get_con","text":"","code":"get_con(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_con.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_con — get_con","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":null,"dir":"Reference","previous_headings":"","what":"get_dbdir — get_dbdir","title":"get_dbdir — get_dbdir","text":"get_dbdir","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_dbdir — get_dbdir","text":"","code":"get_dbdir(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_dbdir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_dbdir — get_dbdir","text":"dbMatrix","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":null,"dir":"Reference","previous_headings":"","what":"get_tblName — get_tblName","title":"get_tblName — get_tblName","text":"get_tblName","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_tblName — get_tblName","text":"","code":"get_tblName(dbMatrix)"},{"path":"https://drieslab.github.io/dbMatrix/reference/get_tblName.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_tblName — get_tblName","text":"dbData","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbDataFrame-method.html","id":null,"dir":"Reference","previous_headings":"","what":"head — head,dbDataFrame-method","title":"head — head,dbDataFrame-method","text":"head","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbDataFrame-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"head — head,dbDataFrame-method","text":"","code":"# S4 method for dbDataFrame head(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"head — head,dbMatrix-method","title":"head — head,dbMatrix-method","text":"head","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/head-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"head — head,dbMatrix-method","text":"","code":"# S4 method for dbMatrix head(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/hidden_aliases.html","id":null,"dir":"Reference","previous_headings":"","what":"rowSums — [,dbData,missing,missing,missing-method","title":"rowSums — [,dbData,missing,missing,missing-method","text":"rowSums rowSums colSums colSums rowMeans rowMeans colMeans colMeans colSds colSds rowSds rowSds mean mean Transpose nrow ncol ncol ncol dim","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/hidden_aliases.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rowSums — [,dbData,missing,missing,missing-method","text":"","code":"# S4 method for dbData,missing,missing,missing [(x, i, j)  # S4 method for dbData,missing,missing,ANY [(x, i, j) <- value  # S4 method for dbMatrix,dbIndex,missing,missing [(x, i, j, ..., drop = TRUE)  # S4 method for dbMatrix,missing,dbIndex,missing [(x, i, j, ..., drop = TRUE)  # S4 method for dbMatrix,dbIndex,dbIndex,missing [(x, i, j, ..., drop = TRUE)  # S4 method for dbDataFrame,dbIndex,missing,ANY [(x, i, j, ..., drop = TRUE)  # S4 method for dbDataFrame,missing,dbIndex,ANY [(x, i, j, ..., drop = TRUE)  # S4 method for dbDataFrame,dbIndex,dbIndex,ANY [(x, i, j, ..., drop = FALSE)  # S4 method for dbDataFrame,missing,missing,missing [(x, i, j)  # S4 method for dbDataFrame,missing,missing,ANY [(x, i, j) <- value  # S4 method for dbDataFrame names(x)  # S4 method for dbDataFrame,dbIndex names(x) <- value  # S4 method for dbData rownames(x)  # S4 method for dbMatrix rownames(x)  # S4 method for dbMatrix rownames(x) <- value  # S4 method for dbData colnames(x)  # S4 method for dbMatrix colnames(x)  # S4 method for dbMatrix,ANY colnames(x) <- value  # S4 method for dbDataFrame,dbIndex colnames(x) <- value  # S4 method for dbMatrix dimnames(x)  # S4 method for dbMatrix,list dimnames(x) <- value  # S4 method for dbDataFrame dimnames(x)  # S4 method for dbDataFrame,list dimnames(x) <- value  # S4 method for dbMatrix,ANY Arith(e1, e2)  # S4 method for ANY,dbMatrix Arith(e1, e2)  # S4 method for dbMatrix,dbMatrix Arith(e1, e2)  # S4 method for dbMatrix,ANY Ops(e1, e2)  # S4 method for ANY,dbMatrix Ops(e1, e2)  # S4 method for dbMatrix,dbMatrix Ops(e1, e2)  # S4 method for dbDenseMatrix rowSums(x, ...)  # S4 method for dbSparseMatrix rowSums(x, ...)  # S4 method for dbDenseMatrix colSums(x, ...)  # S4 method for dbSparseMatrix colSums(x, ...)  # S4 method for dbDenseMatrix rowMeans(x, ...)  # S4 method for dbSparseMatrix rowMeans(x, ...)  # S4 method for dbDenseMatrix colMeans(x, ...)  # S4 method for dbSparseMatrix colMeans(x, ...)  # S4 method for dbDenseMatrix colSds(x, ...)  # S4 method for dbSparseMatrix colSds(x, ...)  # S4 method for dbDenseMatrix rowSds(x, ...)  # S4 method for dbSparseMatrix rowSds(x, ...)  # S4 method for dbDenseMatrix mean(x, ...)  # S4 method for dbSparseMatrix mean(x, ...)  # S4 method for dbMatrix t(x)  # S4 method for dbDataFrame nrow(x)  # S4 method for dbMatrix ncol(x)  # S4 method for dbDataFrame ncol(x)  # S4 method for dbDataFrame ncol(x)  # S4 method for dbMatrix dim(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow.html","id":null,"dir":"Reference","previous_headings":"","what":"The number of rows/cols — nrow","title":"The number of rows/cols — nrow","text":"nrow ncol return number rows columns present x.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/nrow.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The number of rows/cols — nrow","text":"","code":"# S4 method for dbMatrix nrow(x)"},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate array for pretty printing of matrix values — print_array","title":"Generate array for pretty printing of matrix values — print_array","text":"Generate array pretty printing matrix values","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate array for pretty printing of matrix values — print_array","text":"","code":"print_array(   i = NULL,   j = NULL,   x = NULL,   dims,   rownames = rep(\"\", dims[1]),   fill = \".\",   digits = 5L )"},{"path":"https://drieslab.github.io/dbMatrix/reference/print_array.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate array for pretty printing of matrix values — print_array","text":", j, x matched vectors integers j, value x dims dimensions array (integer vector 2) fill fill character digits default = 5. numeric, round number digits","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":null,"dir":"Reference","previous_headings":"","what":"sim_dgc — sim_duckdb","title":"sim_dgc — sim_duckdb","text":"Simulate dbSparseMatrix memory Simulate dbDenseMatrix memory.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"sim_dgc — sim_duckdb","text":"","code":"sim_duckdb(value = datasets::iris, name = \"test\", con = NULL, memory = TRUE)  sim_dgc(num_rows = 50, num_cols = 50, n_vals = 50)  sim_denseMat(num_rows = 50, num_cols = 50)  sim_ijx_matrix(mat_type = NULL, num_rows = 50, num_cols = 50, seed_num = 42)  sim_dbDataFrame(value = NULL, name = \"df_test\", key = NA_character_)  sim_dbSparseMatrix(   num_rows = 50,   num_cols = 50,   seed_num = 42,   name = \"sparse_test\",   memory = FALSE )  sim_dbDenseMatrix(   num_rows = 50,   num_cols = 50,   seed_num = 42,   name = \"dense_test\",   memory = FALSE )"},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"sim_dgc — sim_duckdb","text":"num_rows number rows matrix (default: 50) num_cols number columns matrix (default: 50) seed_num seed number reproducibility (default: 42)","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"sim_dgc — sim_duckdb","text":"dgCMatrix object","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"sim_dgc — sim_duckdb","text":"function generates simulated sparse matrix (dgCMatrix) number rows columns sets n_vals random values non-zero value. function generates simulated dense matrix object specified number rows columns. function generates ijx representation simulated dgCMatrix object specified number rows columns sets 50 random values non-zero value.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"sim_dgc — sim_duckdb","text":"sim_duckdb(): Simulate duckdb connection dplyr tbl_Pool memory sim_dgc(): Simulate dgcMatrix sim_denseMat(): Simulate dense matrix sim_ijx_matrix(): Simulate duckdb connection dplyr tbl_Pool memory sim_dbDataFrame(): Simulate dbDataFrame memory sim_dbSparseMatrix(): Simulate dbSparseMatrix memory sim_dbDenseMatrix(): Simulate dbDenseMatrix memory","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/simulate_objects.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"sim_dgc — sim_duckdb","text":"","code":"sim_ijx_matrix() #> Error in sim_ijx_matrix(): could not find function \"sim_ijx_matrix\""},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbDataFrame-method.html","id":null,"dir":"Reference","previous_headings":"","what":"tail — tail,dbDataFrame-method","title":"tail — tail,dbDataFrame-method","text":"tail","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbDataFrame-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tail — tail,dbDataFrame-method","text":"","code":"# S4 method for dbDataFrame tail(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbMatrix-method.html","id":null,"dir":"Reference","previous_headings":"","what":"tail — tail,dbMatrix-method","title":"tail — tail,dbMatrix-method","text":"tail","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/tail-dbMatrix-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tail — tail,dbMatrix-method","text":"","code":"# S4 method for dbMatrix tail(x, n = 6L, ...)"},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"Convert dbSparseMatrix dbDenseMatrix.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"","code":"toDbDense(db_sparse)"},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"db_sparse dbSparseMatrix object.","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/toDbDense.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert dbSparseMatrix to dbDenseMatrix — toDbDense","text":"","code":"TODO #> Error in eval(expr, envir, enclos): object 'TODO' not found"},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":null,"dir":"Reference","previous_headings":"","what":"to_ijx_disk — to_ijx_disk","title":"to_ijx_disk — to_ijx_disk","text":"to_ijx_disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"to_ijx_disk — to_ijx_disk","text":"","code":"to_ijx_disk(con, name)"},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"to_ijx_disk — to_ijx_disk","text":"con duckdb connection name name table convert ijx disk","code":""},{"path":"https://drieslab.github.io/dbMatrix/reference/to_ijx_disk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"to_ijx_disk — to_ijx_disk","text":"remote table long format unpivoted wide format matrix","code":""},{"path":[]},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"bug-fixes-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Rename update dbIndex superclass fix indexing bugs.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"features-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Features","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Add experimental as_matrix() convenience function.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"chore-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Chore","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Update docs. Migrate site link drieslab. Move {Matrix} Imports.","code":""},{"path":"https://drieslab.github.io/dbMatrix/news/index.html","id":"documentation-0-0-0-9013","dir":"Changelog","previous_headings":"","what":"Documentation","title":"dbMatrix 0.0.0.9013 (2024-01-18)","text":"Update overview.Rmd. 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