gsrc (version 1.1)

cnv: Copy Number Variation

Description

Assign copy number variations (duplications and deletions) based on the a threshold. The CNVs are assigned to all SNPs in a CNV segment. The CNV segments can be calculated using segm.

Usage

cnv(dat, del = -0.1, dup = 0.1)

Arguments

dat

List object, containing at least two matrices "baf" and "rratio" and two vectors "chr" and "pos".

del

Lower threshold, everything below is called deletion.

dup

Upper threshold, everything above is called duplication.

Examples

## Not run: 
# if(require(brassicaData)){
# data("raw_napus", package = "brassicaData", envir = environment())
# dat <- intens_theta(raw_napus)
# dat <- remove_suffix(dat, "_Grn")
# dat <- geno_baf_rratio(dat, delthresh = 11)
# dat <- segm(dat)
# dat <- cnv(dat, dup = 0.03, del = -0.06)
# }
# ## End(Not run)