toBED {DEWSeq}R Documentation

windows/regions to BED

Description

given output of extractRegions, resultsDEWSeq and significance thresholds, extract significant windows, create regions by merging adjacent significant windows. Finally, write the output as a BED file for visualization.

Usage

toBED(windowRes, regionRes, fileName, padjCol = "padj",
  padjThresh = 0.05, log2FoldChangeCol = "log2FoldChange",
  log2FoldChangeThresh = 1, trackName = "sliding windows",
  description = "sliding windows")

Arguments

windowRes

data.frame, output from resultsDEWSeq

regionRes

data.frame, output from extractRegions

fileName

character, filename to save BED output

padjCol

character, name of the adjusted pvalue column (default: padj)

padjThresh

numeric, threshold for p-adjusted value (default: 0.05)

log2FoldChangeCol

character, name of the log2foldchange column (default: log2FoldChange)

log2FoldChangeThresh

numeric, threshold for log2foldchange value (default:1)

trackName

character, name of this track, for visualization

description

character, description of this track, for visualization

Value

write to file

Examples


data(slbpRegions)
data(slbpWindows)
outFile <- tempfile('SLBP_visualization.bed')
# the results are written to a temp file in this example
toBED(slbpWindows,slbpRegions,outFile,padjCol='pSlidingWindows.adj')
[Package DEWSeq version 1.2.0 Index]