crossCorrByExtensionFull: Measure cross correlation using specified frag_len for all...

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

Description

Measure cross correlation using specified frag_len for all regions

Usage

crossCorrByExtensionFull(bam_file, query_gr, frag_len, max_dupes = 1,
  ncores = 1, output_withGRanges = TRUE)

Arguments

bam_file	character. Path to .bam file, must have index at .bam.bai.
query_gr	GRanges. Regions to calculate cross correlation for.
frag_len	integer. Fragment length to calculate cross correlation for.
max_dupes	integer. Duplicate reads above this value will be removed.
ncores	integer. ncores to use to split up the cross correlation calculation.
output_withGRanges	logical. Should results be merged back into query_gr? If TRUE output is GRanges. If FALSE output is data.table.

Value

Either a GRanges equivalent to query_gr with added columns for correlation metics or a data.table of metrics.

Examples

bam_file = system.file("extdata", "MCF10A_CTCF.random5.bam", package = "peakrefine")
np = system.file("extdata", "MCF10A_CTCF.random5.narrowPeak", package = "peakrefine")
qgr = rtracklayer::import(np, format = "narrowPeak")
crossCorrByExtensionFull(bam_file, qgr[1:2], frag_len = 150, ncores = 2)

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