dT2_computeMatrix: dT2 computeMatrix

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

Description

Wrapper for deepTools2 computeMatrix

Usage

dT2_computeMatrix(bigwig_files, bed_files, scale_regions = F,
  ref_point = "TSS", bin_size = 10, upstream_bp = 1, downstream_bp = 1,
  missingDataAsZero = T, skipZeros = T, blacklist_file = NULL, output_gz,
  outFileMatrix = NULL, outSortedRegions = NULL, run_as_sys = F)

Arguments

bigwig_files	vector of bigwig filepaths
bed_files	vector of bed filepaths
scale_regions	use scale-regions mode?
ref_point	if using reference-point mode; "TSS","TES",or "center"
bin_size	size of the bins to use
upstream_bp	how many bases upstream?
downstream_bp	how many bases downstream
missingDataAsZero	Treat missing data as zero?
skipZeros	skip zeros?
blacklist_file	use a blacklist file?
output_gz	filepath to the output .gz file
outFileMatrix	filepath to the output .tab file for underlying values
outSortedRegions	filepath to a bed file for outputting sorted regions.
run_as_sys	Return the command as a string or run as system

Value

RETURN_DESCRIPTION

Examples

# ADD_EXAMPLES_HERE

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