cnv: Copy Number Variation

In gsrc: Genome Structure Rearrangement Calling in Genomes with High Synteny

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)

Example output

Loading required package: brassicaData
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'brassicaData'

gsrc documentation built on May 30, 2017, 4:16 a.m.