prepare_elements: Preparation of elements and active sites for ActiveDriverWGS...

In reimandlab/ActiveDriverWGS: Whole Genome Cancer Driver Discovery

Description

Preparation of elements and active sites for ActiveDriverWGS analysis with the find_drivers function

Usage

prepare_elements(elements_file, sites_file, window_size = 50000,
  mc.cores = 1, recovery_dir = NA)

Arguments

elements_file	path to a BED12 file of the elements to analyze
sites_file	path to a BED4 file of active sites to use in the analysis
window_size	numeric value for the size of the background sequence window to use on each side of the given elements. Default value is 50000.
mc.cores	numeric indicating the number of computing cores to use. Default value is 1.
recovery_dir	path to a directory for ActiveDriverWGS to store intermediate computations in. In the case that prepare_elements does not complete, run it again with the same value for this parameter, and it will read the intermediate computations rather than compute them again. Please specify a different directory, or delete the ActiveDriverWGS data in a previously used directory, if running with different data. Default value is NA, and prepare_elements will not save any intermediate information with this value.

Value

list containing element and active site information needed for ActiveDriverWGS analysis

reimandlab/ActiveDriverWGS documentation built on May 16, 2019, 7:47 a.m.