pct.genome.changed: Calculate the percentage of genome changed by CNV
In gonzolgarcia/svcnvplus: Integrative analyses of CNV segmentation and SV variant calls

Calculate the percentage of genome changed by CNV

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

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

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

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

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

pct.genome.changed(cnv)

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

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