dT2_bamCoverage: dT2 bamCoverage

In avhgenomics/bioKIT: bioKIT: Common functions for routine molecular biology applications.

Description

Wrapper for deepTools2 bamCoverage; converts a bam file to a bigwig / bedgraph for use in visualization and analysis.

Usage

dT2_bamCoverage(bam_file, output_file, outFileFormat = "bigwig",
  scaleFactor = NULL, binSize = 10, region = NULL,
  blacklist_file = NULL, effectiveGenomeSize = NULL,
  normalizeUsing = NULL, smoothLength = NULL, extendReads = NULL,
  processors = "max", ignoreDuplicates = T, run_as_sys = F)

Arguments

bam_file	DESCRIPTION.
output_file	DESCRIPTION.
outFileFormat	DESCRIPTION.
scaleFactor	DESCRIPTION.
binSize	DESCRIPTION.
region	DESCRIPTION.
blacklist_file	DESCRIPTION.
effectiveGenomeSize	DESCRIPTION.
normalizeUsing	DESCRIPTION.
smoothLength	DESCRIPTION.
extendReads	DESCRIPTION.
processors	DESCRIPTION.
ignoreDuplicates	DESCRIPTION.
run_as_sys	DESCRIPTION.

Value

RETURN_DESCRIPTION

Examples

# ADD_EXAMPLES_HERE

avhgenomics/bioKIT documentation built on May 5, 2019, 12:29 a.m.