macs2gr {TransView} | R Documentation |
Parses the output of MACS Peak finding algorithm and returns a GRanges object compatible to the down stream functions of TransView
macs2gr(macs_peaks_xls, psize, amount="all", min_pileup=0, log10qval=0, log10pval=0, fenrichment=0, peak_mid="summit")
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 |
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 |
Convenience function parsing the output of a MACS file. Tested with MACS v1.4 and v.2.09
GRanges
object with one row per peak and meta data score, enrichment and log10 pvalue.
Julius Muller ju-mu@alumni.ethz.ch
exls<-dir(system.file("extdata", package="TransView"),full=TRUE,patt="xls$") peaks<-macs2gr(exls,psize=500) head(peaks)