multicoco: Multi-scale coverage correction

In mskilab/fragCounter: GC mappability correction and segmentation

Multi-scale coverage correction

Description

Given gc and mappability coverage correction at k "nested" scales finds the coverage assignment at the finest scale that yields the best correction at every scale

Usage

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

Arguments

cov	GRanges constant with GRanges of coverage samples with (by default) fields $reads, $map, $gc
numlevs	integer numbers of scales at which to correct
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
mono	boolean Wether to only do single iteration at finest scale
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, perform correction using exons as bins instead of fixed size

Author(s)

Marcin Imielinski

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