addCovToGR: Add coverage to regions in 'GRanges' object.

In sevenC: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Description

This function adds a NumericList of coverage (or any other signal in the input bigWig file) to each range in a GRanges object. The coverage is reported for a fixed-sized window around the region center. For regions with negative strand, the coverage vector is reversed. The coverage signal is added as new metadata column holding a NumericList object. Note, this function does not work on windows because reading of bigWig files is currently not supported on windows.

Usage

addCovToGR(gr, bwFile, window = 1000, binSize = 1, colname = "chip")

Arguments

gr	GRanges object with genomic regions. It should contain a valid seqinfo object with defined seqlengths.
bwFile	File path or connection to BigWig or wig file with coverage to parse from.
window	Numeric scalar for window size around the center of ranges in gr.
binSize	Integer scalar as size of bins to which the coverage values are combined.
colname	Character as name of the new column that is created in gr.

Value

GRanges as input but with an additional meta column containing the coverage values for each region as NumericList.

Examples

if (.Platform$OS.type != "windows") {

 # use example bigWig file of ChIP-seq signals on human chromosome 22
 exampleBigWig <- system.file("extdata",
 "GM12878_Stat1.chr22_1-30000000.bigWig", package = "sevenC")

 # use example CTCF moitf location on human chromosome 22
 motifGR <- sevenC::motif.hg19.CTCF.chr22

 # add ChIP-seq signals to motif regions
 motifGR <- addCovToGR(motifGR, exampleBigWig)

 # add ChIP-seq signals as column named "Stat1"
 motifGR <- addCovToGR(motifGR, exampleBigWig, colname = "Stat1")

 # add ChIP-seq signals in windows of 500bp around motif centers
 motifGR <- addCovToGR(motifGR, exampleBigWig, window = 500)

 # add ChIP-seq signals in bins of 10 bp
 motifGR <- addCovToGR(motifGR, exampleBigWig, binSize = 10)

}

sevenC documentation built on Nov. 8, 2020, 5:35 p.m.