TransView (version 1.16.0)

macs2gr: Convenience function for MACS output conversion

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.

Value

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

Details

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

Examples

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

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