segment.gap: Fills the gaps in a segmentation data.frame. Chromosome...

In gonzolgarcia/svcnvplus: Integrative analyses of CNV segmentation and SV variant calls

Description

Fills the gaps in a segmentation data.frame. Chromosome limits are defined for the complete segmentation dataset then segments fill the missing terminal regions. The CN log-ratio of the added segments is set to the average of the closest neighbours in each sample.

Usage

segment.gap(cnv, chrlist = NULL, verbose = FALSE)

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' validated by validate.cnv
chrlist	(character) list of chromosomes to include chr1, chr2, etc...
verbose	(logical)

Value

a data.frame containing CNV data

Examples

## validate input data.frames
cnv <- validate.cnv(segdat_lung_ccle)

segment.gap()

gonzolgarcia/svcnvplus documentation built on March 4, 2020, 6:02 p.m.