correctcov_stub: Correct coverage stub

In kcygan/fragCounter: GC mappability correction and segmentation

Description

prepares GC, mappability, and coverage files for multicoco

Usage

correctcov_stub(cov.wig, mappability = 0.9, samplesize = 50000,
  verbose = T, gc.rds.dir, map.rds.dir, exome = FALSE)

Arguments

cov.wig	wig file of coverage tiles of width W or pointer to rds file of sorted GRanges object or GRanges object
mappability	double threshold for mappability score
samplesize	integer size of sub-sample
verbose	boolean Wether to print log to console
gc.rds.dir	string for tiles of width W, will look here for a file named gcW.rds in this directory
map.rds.dir	string for tiles of width W will look here for a file named mapW.rds in this directory
exome	boolean If TRUE, look in gc/map.rds.dir for files called 'gcexome.rds' and 'mapexome.rds'

Author(s)

Trent Walradt

kcygan/fragCounter documentation built on Feb. 13, 2020, 12:34 a.m.