toBED: windows/regions to BED

In EMBL-Hentze-group/DEWSeq: Differential Expressed Windows Based on Negative Binomial Distribution

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')

EMBL-Hentze-group/DEWSeq documentation built on Oct. 17, 2023, 10:41 p.m.