segment.gap: CNV segmentation gap filling

In ccbiolab/svpluscnv: svpluscnv: analysis and visualization of complex structural variation data

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, minsize = 5000, chrlist = NULL, verbose = FALSE)

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' initialized by validate.cnv
minsize	(numeric) the minimum gap size required to fill the gap
chrlist	(character) list of chromosomes to include chr1, chr2, etc...
verbose	(logical) whether to return internal messages

Value

a data.frame containing CNV data

Examples

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

cnv2 <- segment.gap(cnv)
cnv2

ccbiolab/svpluscnv documentation built on Sept. 9, 2020, 4:52 a.m.