gene.cnv: Obtain a matrix with the weighted average CN per chromosome...

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

Description

Obtain a matrix with the weighted average CN per chromosome arm

Usage

gene.cnv(
  cnv,
  genome.v = "hg19",
  genesgr = NULL,
  chrlist = NULL,
  fill.gaps = FALSE,
  verbose = TRUE
)

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' validated by validate.cnv
genome.v	(hg19 or hg38) reference genome version to draw chromosome limits and centromeres
genesgr	(S4) a GenomicRanges object containing gene annotations (if not NULL overides genome.v). It must containg 'strand' and a metadata field 'gene_id' with unique values. Seqnames are expected in the format (chr1, chr2, ...)
chrlist	(character) list of chromosomes to include chr1, chr2, etc...
verbose	(logical)
fill	(logical) whether to fill the gaps in the segmentation file using gap neighbour segmean average as log ratio

Value

an instance of the class 'genecnv' containing gene level copy number info

Examples

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

gene.cnv(cnv)

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