diff --git a/R/BSmooth.tstat.R b/R/BSmooth.tstat.R index d852073..c8c16bc 100644 --- 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 index ddba61f..3fc3775 100644 --- a/inst/NEWS.Rd +++ b/inst/NEWS.Rd @@ -3,18 +3,25 @@ \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. } \item{Minor code and documentation chnages. Fixed usage of - \code{class(x) == "y"} and added examples to some man pages.} - \item{\code{Bsseq()} is modified to store filtered matrix (ambigious modification status) for nanopore data. - } - \item{New function \code{read.modkit()} to read in methyl bed files generated from modkit and construct Bsseq objects. When there is no other modifications, one Bsseq object is constructed, and when there is other modification present, its methylation and corresponding coverage are also stored - and two Bsseq objects are constructed. - } - \item{New function \code{read.modbam2bed()} to read in, extract methylation, coverage and filtered data and create Bsseq object from methyl bed files obtained by modbam2bed. Some instructions for using modbam2bed is also provided. - } + \code{class(x) == "y"} and added examples to some man pages.} + \item{\code{Bsseq()} is modified to store filtered matrix (ambigious + modification status) for nanopore data.} + \item{New function \code{read.modkit()} to read in methyl bed files + generated from modkit and construct Bsseq objects. When there is + no other modifications, one Bsseq object is constructed, and when + there is other modification present, its methylation and + corresponding coverage are also stored and two Bsseq objects are + constructed. } + \item{New function \code{read.modbam2bed()} to read in, extract + methylation, coverage and filtered data and create Bsseq object + from methyl bed files obtained by modbam2bed. Some instructions + for using modbam2bed is also provided.} } }