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

Description Usage Arguments Details

View source: R/extract_summary.R

Description

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

Usage

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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.