diff --git a/DESCRIPTION b/DESCRIPTION index f9576fe..851dbc4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: raer Type: Package Title: RNA editing tools in R -Version: 1.0.1 +Version: 1.0.2 Authors@R: c( person("Kent", "Riemondy", , "kent.riemondy@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0750-1273")), @@ -65,7 +65,7 @@ SystemRequirements: VignetteBuilder: knitr Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 URL: https://rnabioco.github.io/raer, https://github.com/rnabioco/raer BugReports: https://github.com/rnabioco/raer/issues biocViews: diff --git a/man/find_de_sites.Rd b/man/find_de_sites.Rd index 098346c..17d111a 100644 --- a/man/find_de_sites.Rd +++ b/man/find_de_sites.Rd @@ -66,9 +66,10 @@ rse$condition <- substr(rse$sample, 1, 2) rse <- calc_edit_frequency(rse) dse <- make_de_object(rse) -res <- find_de_sites(dse, - condition_control = "WT", - condition_treatment = "KO") +res <- find_de_sites(dse, + condition_control = "WT", + condition_treatment = "KO" +) res$sig_results[1:3, ] } diff --git a/man/pileup_cells.Rd b/man/pileup_cells.Rd index 4964916..fd50674 100644 --- a/man/pileup_cells.Rd +++ b/man/pileup_cells.Rd @@ -113,13 +113,18 @@ sce many_small_bams <- rep(bam_fn, 10) bam_ids <- LETTERS[1:10] + +# for unstranded libraries, sites and alleles should be provided on + strand +gr <- GRanges(c("2:579:+", "2:625:+", "2:645:+", "2:589:+", "2:601:+")) +gr$REF <- c(rep("T", 4), "A") +gr$ALT <- c(rep("C", 4), "G") fp <- FilterParam( library_type = "unstranded", remove_overlaps = TRUE ) -pileup_cells(many_small_bams, +sce <- pileup_cells(many_small_bams, sites = gr, cell_barcodes = bam_ids, cb_tag = NULL, @@ -127,6 +132,7 @@ pileup_cells(many_small_bams, outdir, param = fp ) +sce unlink(bai) diff --git a/man/raer.Rd b/man/raer.Rd index ff36a1f..f8afa4b 100644 --- a/man/raer.Rd +++ b/man/raer.Rd @@ -2,8 +2,8 @@ % Please edit documentation in R/raer.R \docType{package} \name{raer} -\alias{raer} \alias{raer-package} +\alias{raer} \title{raer: RNA editing tools in R} \description{ \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}}