From bdca54debfcc9f96fd5cc0843197d916981dc2c5 Mon Sep 17 00:00:00 2001
From: Xiuwen Zheng <zhengxwen@users.noreply.github.com>
Date: Wed, 3 Jan 2024 17:58:32 -0600
Subject: [PATCH] tweak help file

---
 DESCRIPTION          |  4 ++--
 NEWS                 |  8 ++++++++
 README.md            |  4 ++--
 man/seqBlockApply.Rd | 11 +++--------
 4 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5b1c9ed..a9350e1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: SeqArray
 Type: Package
 Title: Data Management of Large-Scale Whole-Genome Sequence Variant Calls
-Version: 1.41.4
-Date: 2023-10-20
+Version: 1.43.1
+Date: 2024-01-04
 Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1)
 Imports: methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings,
         S4Vectors
diff --git a/NEWS b/NEWS
index 5c1eca6..b4d02e6 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,11 @@
+CHANGES IN VERSION 1.43.1
+-------------------------
+
+UTILITIES
+
+    o update the help file of `seqBlockApply()`
+
+
 CHANGES IN VERSION 1.42.0
 -------------------------
 
diff --git a/README.md b/README.md
index 9382758..0b1c0ad 100644
--- a/README.md
+++ b/README.md
@@ -18,7 +18,7 @@ The SeqArray package is built on top of [Genomic Data Structure (GDS)](https://g
 
 ## Bioconductor:
 
-Release Version: v1.38.0
+Release Version: v1.42.0
 
 [http://www.bioconductor.org/packages/release/bioc/html/SeqArray.html](http://www.bioconductor.org/packages/SeqArray)
 
@@ -26,7 +26,7 @@ Release Version: v1.38.0
 * Tutorials: [Data Management](http://www.bioconductor.org/packages/release/bioc/vignettes/SeqArray/inst/doc/SeqArrayTutorial.html), [R Integration](http://www.bioconductor.org/packages/release/bioc/vignettes/SeqArray/inst/doc/SeqArray.html), [Overview Slides](http://www.bioconductor.org/packages/release/bioc/vignettes/SeqArray/inst/doc/OverviewSlides.html)
 * [News](http://www.bioconductor.org/packages/release/bioc/news/SeqArray/NEWS)
 
-Development Version: v1.39.0
+Development Version: v1.43.1
 
 [http://www.bioconductor.org/packages/devel/bioc/html/SeqArray.html](http://www.bioconductor.org/packages/devel/bioc/html/SeqArray.html)
 
diff --git a/man/seqBlockApply.Rd b/man/seqBlockApply.Rd
index 0d982b7..b745729 100644
--- a/man/seqBlockApply.Rd
+++ b/man/seqBlockApply.Rd
@@ -61,6 +61,9 @@ associated with these variables.
 \code{"$dosage_alt"} returns a RAW/INTEGER matrix for the dosages of alternative
 allele without distinguishing different alternative alleles.
 
+\code{"$dosage_sp"} returns a sparse matrix (dgCMatrix) for the dosages of
+alternative allele without distinguishing different alternative alleles.
+
 \code{"$num_allele"} returns an integer vector with the numbers of distinct
 alleles.
 
@@ -106,19 +109,11 @@ the high-speed memory instead of disk.
 # get 'variant.id'
 head(variant.id <- seqGetData(f, "variant.id"))
 
-
 # set sample and variant filters
 set.seed(100)
 seqSetFilter(f, sample.id=samp.id[c(2,4,6,8,10)],
     variant.id=sample(variant.id, 10))
 
-# read
-seqApply(f, "genotype", FUN=print, margin="by.variant")
-seqApply(f, "genotype", FUN=print, margin="by.variant", .useraw=TRUE)
-
-seqApply(f, "genotype", FUN=print, margin="by.sample")
-seqApply(f, "genotype", FUN=print, margin="by.sample", .useraw=TRUE)
-
 # read in block
 seqGetData(f, "$dosage")
 seqBlockApply(f, "$dosage", print, bsize=3)