superFreq (version 1.2.3)

importCaptureRegions: Imports capture regions from a bed file with GC information.

Description

Imports capture regions from a bed file with GC information.

Usage

importCaptureRegions(bedFile, reference, Rdirectory, genome = "hg19",
  forceRedoCR = F, forceRedoRdirectorySave = F)

Arguments

genome

Which genome the bed file is on. 'hg19', 'hg38' and 'mm10' only supported atm.

file

Bedfile of the capture regions with extra columns for gc and binding strength information.

gcColumn

the column in the bed file that contains the gc content. Default 5 matches output from the provided script at X.

dnColumn

the column in the bed file that contains the binding strength. Default 6 matches output from the provided script at X.

Details

Reads in the bed file into GRanges format, with extra columns for GC and binding strength.

Examples

# NOT RUN {
captureRegions = importCaptureRegions('path/to/my/captureRegions.bed')
plotColourScatter(captureRegions$gc, captureRegions$dn, xlab='GC content', ylab='binding strength')

# }