Merge branch 'devel' into update-other-mod

hansenlab · Apr 3, 2024 · 5b64dfe · 5b64dfe
2 parents c0c1f9e + 1b70d4d
commit 5b64dfe
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Showing 4 changed files with 5 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: bsseq
-Version: 1.39.2
+Version: 1.39.3
 Encoding: UTF-8
 Title: Analyze, manage and store whole-genome methylation data
 Description: A collection of tools for analyzing and visualizing whole-genome

diff --git a/R/BSmooth.tstat.R b/R/BSmooth.tstat.R
@@ -1,5 +1,5 @@
 BSmooth.tstat <- function(BSseq, group1, group2, estimate.var = c("same", "paired", "group2"),
-                          local.correct = TRUE, maxGap = NULL, qSd = 0.75, k = 101, mc.cores = 1, verbose = TRUE){
+                          local.correct = TRUE, maxGap = NULL, qSd = 0.75, k = 21, mc.cores = 1, verbose = TRUE){
     smoothSd <- function(Sds, k) {
         k0 <- floor(k/2)
         if(all(is.na(Sds))) return(Sds)

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -3,6 +3,8 @@
 \encoding{UTF-8}
 \section{Version 1.39.x}{
   \itemize{
+    \item{Changing the default value of k in \code{BSmooth.tstat} from
+      \code{k=101} to \code{k=21}.}
     \item{Removed \code{read.umtab}, \code{read.bsmooth}. The alignment
       program which produced these files have not been supported for
       years. }
@@ -19,7 +21,6 @@
       coverage and filtered data and create Bsseq object from methyl bed files 
       obtained by modbam2bed. Some instructions for using modbam2bed is also provided.
          }
-  }
 }
 
 

diff --git a/man/BSmooth.tstat.Rd b/man/BSmooth.tstat.Rd
@@ -11,7 +11,7 @@
 \usage{
 BSmooth.tstat(BSseq, group1, group2,
   estimate.var = c("same", "paired", "group2"), local.correct = TRUE,
-  maxGap = NULL, qSd = 0.75, k = 101, mc.cores = 1, verbose = TRUE)
+  maxGap = NULL, qSd = 0.75, k = 21, mc.cores = 1, verbose = TRUE)
 }
 \arguments{
   \item{BSseq}{An object of class \code{BSseq}.}