macs2gr: Convenience function for MACS output conversion

In TransView: Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

Description

Parses the output of MACS Peak finding algorithm and returns a GRanges object compatible to the down stream functions of TransView

Usage

macs2gr(macs_peaks_xls, psize, amount="all", min_pileup=0, log10qval=0, log10pval=0, fenrichment=0, peak_mid="summit")

Arguments

macs_peaks_xls	Full path to the file ending with ‘_peaks.xls’ located in the output folder of a MACS run.
psize	An integer setting the total length of the peaks. Setting psize to ‘preserve’ will keep the original peak lengths from the output file and override peak_mid. Note that this is not compatible with plotTV
amount	Amount of peaks returned. If an integer is provided, the returned peaks will be limited to this amount after sorting by pile up score.
min_pileup	Minimum pile up.
log10qval	Minimal log10 q-value
log10pval	Minimal log10 p-value
fenrichment	Minimal enrichment.
peak_mid	If set to ‘summit’, the peaks with length psize will centered on the peak summit. If set to ‘center’, the mid point of start and end will be used.

Details

Convenience function parsing the output of a MACS file. Tested with MACS v1.4 and v.2.09

Value

GRanges object with one row per peak and meta data score, enrichment and log10 pvalue.

Author(s)

Julius Muller [e-mail]

Examples

exls<-dir(system.file("extdata", package="TransView"),full=TRUE,patt="xls$")

peaks<-macs2gr(exls,psize=500)
head(peaks)

TransView documentation built on Nov. 8, 2020, 5:31 p.m.