Description Usage Arguments Value Author(s) Examples
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.
1 | compute.absCN(seg.data, alpha.opt, tau.opt, qmax = 7)
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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 |
The input data frame is augmented with two additional columns: rhat (expected copy ratio) and CN (absolute copy number)
Lei Bao
1 2 3 | 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
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