extract_summary: Extract area under the curve for every peak from from given...

In PoisonAlien/peakseason: Functions for faster ChIP/ATAC-seq analysis and visualization.

Description

Extract area under the curve for every peak from from given bigWig files.

Usage

extract_summary(coldata = NULL, bed = NULL, genome = NULL,
  startFrom = NULL, up = 2500, down = 2500, op_dir = "./",
  rmAfter = TRUE, keepBed = TRUE, bwt_path = NULL,
  bedHeader = FALSE, nthreads = 4, remove_dups = FALSE)

Arguments

coldata	Coldata generated from read_coldata
bed	Input bed file. Can also be a gz compressed narrowPeak/BED
genome	can be hg19 or mm10
startFrom	NULL Default is to estimate complete AUC for each BED entry. Can be 'tss', 'tes' or 'center'
up	Default 2500. Only applicable if startFrom is provided.
down	Default 2500. Only applicable if startFrom is provided.
op_dir	Directory to store results. Defult "./"
rmAfter	remove matrix files generated by bwtool once data is read into R. Default TRUE.
keepBed	Keep output BED as is? Default TRUE
bedHeader	Does input BED file has header. Default FALSE
nthreads	Threads to use. Default 4.
remove_dups	Remove duplicated BED entries with same start and end coordinates. Default FALSE.
bw_path	path to bwtool. Default looks under system path.

Details

This function is a wrapper around bwtool summary command and extracts peak intesities from bigWig files for every peak in an input BED file. Once extraction is complete signal values are combined into a single data.table

PoisonAlien/peakseason documentation built on May 14, 2019, 4:01 a.m.