score_motif: Assembles several metrics for a set of peaks from: 1) the...

In jrboyd/peakrefine: Peak Refinement Metric Gathering and Evalutation by Motif Enrichment

Description

Stratify by each metric and conduct motif enrichment for each.

Usage

score_motif(bam_file, bam_input, query_gr, fl, motif_res = NULL,
  pwm = PWMLogn.hg19.MotifDb.Hsap, include_fl_independent = FALSE,
  out_dir = file.path("~/R/peakrefine/cache", sub(".bam", "",
  basename(bam_file))), nbases = 200, ncores = 32)

Arguments

bam_file	character. Path to treatment/ChIP-seq .bam file, must have index at .bam.bai.
bam_input	character. Path to input/non-ChIP control .bam file, must have index at .bam.bai.
query_gr	GRanges. Regions to calculate cross correlation for.
ncores

jrboyd/peakrefine documentation built on July 30, 2020, 7:13 p.m.