gene.cnv: Gene-level CNV

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

Description

Obtains a gene-level copy number matrix from a segmentation profile.

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' initialized by validate.cnv
genome.v	(hg19 or hg38) reference genome version to fetch gene annotations when 'genesgr=NULL'
genesgr	(S4) a GenomicRanges object containing genomic feature 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...
fill.gaps	(logical) whether to fill the gaps in the segmentation file using gap neighbour segmean average as log ratio
verbose	(logical)

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)

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