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

Description Usage Arguments Value Author(s) Examples

View source: R/absCNSeq.R

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

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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

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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.