coco: Coverage correction

In mskilab/fragCounter: GC mappability correction and segmentation

Coverage correction

Description

Given gc and mappability coverage correction, yields corrected read counts

Usage

coco(cov, base = max(10, 1e5/max(width(cov))), fields = c("gc", "map"), iterative = TRUE,
presegment = TRUE, min.segwidth = 5e6, verbose = TRUE,
FUN = NULL, ..., mc.cores = 1, exome = TRUE, imageroot = NULL)

Arguments

cov	GRanges constant with GRanges of coverage samples with (by default) fields $reads, $map, $gc
base	integer Scale multiplier
fields	character vector fields of gc to use as covariates
iterative	boolean whether to iterate
presegment	boolean whether to presegment
min.segwidth	integer when presegmenting, minimum segment width
verbose	boolean Wether to print log to console
FUN	function with which to correct coverage (by default loess correction modified from HMMcopy that takes in granges with fields $reads and other fields specified in "fields"
...	additional args to FUN
mc.cores	integer Number of cores to use
exome	boolean If TRUE, collapse by 1e5 for presegmentation
imageroot	String, optional file root to which to dump images of correction

Author(s)

Trent Walradt

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