get_matrix: Create a matrix with extracted data from a bigWig file within...

In ClaudiaRHD/chipAnalyser: R package for rapid ChIP-seq data analysis and visualisation.

Description

Create a matrix with extracted data from bigWig files. Region around peak which should be observed can be specified. Returns a list with the matrix and the inserted parameters (region, binsize, reference position) and filenames (bed file andbigWig files).

Usage

get_matrix(bed = NULL, bw_files = NULL, bw_path = NULL, op_dir = NULL,
  up = 2500, down = 2500, pos = "", binsize = 25, numcores = NULL)

Arguments

bed	A file in bed format. Default value is NULL.
bw_files	One or a character vector with multiple files in bigWig format. Default value is NULL.
bw_path	The path to directory where bwtool is installed on the computer. Default value is NULL.
op_dir	The path to the operation directory currently used. Default value is NULL.
up	Number of basepairs from peak to 5' end. Default value is 2500.
down	Number of basepairs from peak to 3' end.Default value is 2500.
pos	Reference position of the region around a peak. Possibilities: '-starts' and '-ends'. Default value is ” and means a centered reference position.
binsize	Binsize of how many basepairs the avergae will be calculated. Default value is 25.
numcores	Number of cores which should be used in parallelised process.Default value is NULL and will be defined as the number of available cores - 1.

Value

result list with matrices and additional information about the input of the function

ClaudiaRHD/chipAnalyser documentation built on June 18, 2020, 8:31 p.m.