compute.absCN: Convert copy ratios into abosolute copy numbers when given...

In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description

This function converts copy ratios into abosolute copy numbers when the tumor purity and ploidy are provided by the user. The tumor purity and ploidy parameter should be taken from the result after running the "run.absCNSeq" function.

Usage

compute.absCN(seg.data, alpha.opt, tau.opt, qmax = 7)

Arguments

seg.data	a data frame with five columns: "chrom", "loc.start", "loc.end", "eff.seg.len", "normalized.ratio".
alpha.opt	tumor purity estimate
tau.opt	tumor ploidy estimate
qmax	maximum allowed absolute copy number for any segments

Value

The input data frame is augmented with two additional columns: rhat (expected copy ratio) and CN (absolute copy number)

Author(s)

Lei Bao

Examples

data("absCNseq", package="lxctk")
my.res.list <- run.absCNSeq(cn, snv, "myResult", "Sample1", seq.type="WES", min.seg.len=200)
seg.CN <- compute.absCN(my.res.list$seg.dat, my.res.list$searchRes[i,"alpha"], my.res.list$searchRes[i,"tau"])  # the i-th solution

lixiangchun/lxctk documentation built on May 21, 2019, 6:44 a.m.