amp.del: Amplifications and deletions

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

Description

Retrieve amplification and deletion 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)
lapply(geneampdel,head)

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