amp.del: Retrieve amplification events from a 'genecnv.obj' generated...

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

Description

Retrieve amplification events from a 'genecnv.obj' generated by 'gene.cnv' function

Usage

amp.del(genecnv.obj, logr.cut = 2)

Arguments

genecnv.obj	(genecnv) an instance of the class 'genecnv' containing gene level copy number info
logr.cut	(numeric) the log-ratio cutoff above which genes are considered amplified (e.g 2 = 8 copies for amplification and 0.5 copies for deep deletions, in diploid regions)

Value

(list) A list of lists including amplified.list, amplified.rank, deepdel.list and deepdel.rank

Examples

## validate input data.frames
cnv <- validate.cnv(segdat_lung_ccle)
genecnv.obj <- gene.cnv(cnv)
geneampdel <- amp.del(genecnv.obj, logr.cut = 2)

gonzolgarcia/svpluscnv documentation built on March 4, 2020, 10:06 a.m.