writeBedGraph {PeakSegDisk}

Write bedGraph file

Description

Write a data.frame in R to a bedGraph file on disk. This must be a plain text file with the following four columns: chrom (character chromosome name), chromStart (integer start position), chromEnd (integer end position), count (integer aligned read count on chrom from chromStart+1 to chromEnd); see also https://genome.ucsc.edu/goldenPath/help/bedgraph.html

Usage

writeBedGraph(count.df, 
    coverage.bedGraph)

Arguments

count.df

data.frame with four columns: chrom, chromStart, chromEnd, count.

coverage.bedGraph

file path where data will be saved in plain text / bedGraph format.

Value

NULL (same as write.table).

Author(s)

Toby Dylan Hocking

Examples

library(PeakSegDisk)
data(Mono27ac, envir=environment())
coverage.bedGraph <- file.path(
  tempfile(),
  "H3K27ac-H3K4me3_TDHAM_BP",
  "samples",
  "Mono1_H3K27ac",
  "S001YW_NCMLS",
  "problems",
  "chr11-60000-580000",
  "coverage.bedGraph")
dir.create(
  dirname(coverage.bedGraph),
  recursive=TRUE, showWarnings=FALSE)
writeBedGraph(Mono27ac$coverage, coverage.bedGraph)
fread.first(coverage.bedGraph, col.name.list$coverage)
fread.last(coverage.bedGraph, col.name.list$coverage)