correctcov_stub: Correct coverage stub

In mskilab/fragCounter: GC mappability correction and segmentation

Correct coverage stub

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,
  chr.sub = TRUE
)

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'
chr.sub	boolean if TRUE replace chr prefix in seqnames, default TRUE.

Author(s)

Trent Walradt

mskilab/fragCounter documentation built on Jan. 27, 2024, 2:35 p.m.