Commit 2dba4e68 authored by Sudeep Sahadevan's avatar Sudeep Sahadevan

version number changed to Bioconductor default pre release version number

parent da1c431a
Package: DEWSeq
Type: Package
Title: Differential Expressed Windows Based on Negative Binomial Distribution
Version: 1.6.0
Authors@R: c(
person("Sudeep", "Sahadevan", email="sahadeva@embl.de", role = c("cre")),
person("Thomas", "Schwarzl", email="schwarzl@embl.de", role = c("ctb"))
)
Version: 0.99.0
Author: Sudeep Sahadevan <sahadeva@embl.de>, Thomas Schwarzl <schwarzl@embl.de>
Maintainer: Hentze bioinformatics team <biohentze@embl.de>
Description: Differential expression analysis of windows for next-generation sequencing data like eCLIP or iCLIP data.
Imports:
......
......@@ -17,13 +17,15 @@
#' @param trackName name of this track, for visualization
#' @param description description of this track, for visualization
#'
#' @return write to file
#'
#' @examples
#' # need specific examples
#' \dontrun{
#' 'toBED(windowRes=windowRes,regionRes=regionRes,fileName="enrichedWindowsRegions.bed")'
#' }
#'
#' @return NULL
toBED <- function(windowRes,regionRes,fileName,padjCol='padj',padjThresh=0.05,log2FoldChangeCol='log2FoldChange',log2FoldChangeThresh=1,trackName='sliding windows',
description='sliding windows'){
wRequiredCols <- c('unique_id','chromosome','begin','end','strand',padjCol,log2FoldChangeCol)
......
......@@ -28,6 +28,9 @@ toBED(windowRes, regionRes, fileName, padjCol = "padj",
\item{description}{description of this track, for visualization}
}
\value{
write to file
}
\description{
given output of \code{\link{extractRegions}}, \code{\link{resultsDEWSeq}} and significance thresholds,
extract significant windows, create regions by merging adjacent significant windows.
......
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