toBED: windows/regions to BED

In DEWSeq: Differential Expressed Windows Based on Negative Binomial Distribution

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')

DEWSeq documentation built on Nov. 28, 2020, 2:01 a.m.