pct.genome.changed: Percent genome change calculation

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

Description

Calculates the percentage of genome changed using CNV segmentation profiles. Genome change is defined based on the fold change CNV log-ratio between a sampele and a reference.

Usage

pct.genome.changed(cnv, fc.pct = 0.2, discard.sex = TRUE)

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' initialized by validate.cnv
fc.pct	(numeric) percentage CNV gain/loss for a segment to be considered changed (e.g. 0.2 = 20 percent change 0.8 < segmean && segmean > 1.2)
discard.sex	(logical) whether sex chromosomes should be included

Value

(numeric) vector containing percent genome changed values (0-1)

See Also

Additional data format information in the man pages of validate.cnv

Examples

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

pct_changed <- pct.genome.changed(cnv)
head(pct_changed)

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