extract_matrix: Extract matrix of signal values from given bigWig files...

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

Description

Extract matrix of signal values from given bigWig files around region of interset - bed file.

Usage

extract_matrix(coldata = NULL, bed = NULL, genome = NULL,
  binSize = 25, startFrom = "center", up = 2500, down = 2500,
  k = NULL, op_dir = "./", rmAfter = TRUE, bwt_path = NULL,
  nthreads = 4)

Arguments

coldata	Input coldata generated from read_coldata
bed	Input bed file
genome	Can be hg19 or mm10. Default NULL. If bed and genome arguments are given, bed will be used.
binSize	Default 25bp
startFrom	region of interest. Default from peak 'center'. Can be 'tss' or 'tes'.
up	upsteram in bp. Default 2500.
down	downstream in bp. Default 2500.
k	cluster regions with k-means where k is the number of clusters. Defualt NULL.
op_dir	Directory to store results. Defult "./"
rmAfter	remove matrix files generated by bwtool once data is read into R. Default TRUE.
nthreads	threads to use. Default 4.
bw_path	path to bwtool. Default looks under system path.

Details

This function is a wrapper around bwtool matrix command and extracts signals from bigWig files from an input BED file. Once extraction is complete matrix can be summarized by mean or median signals.

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