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correct CN for low purity samples

Adjusted CN correction for samples to as low as 0.05 purity (0.2 previously).
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gavinha committed Oct 29, 2018
1 parent a5ad26f commit ba8ca730ccfa9580ff58c5fe3d37159809e6ee37
Showing with 1 addition and 1 deletion.
  1. +1 −1 code/combineTITAN-ichor.R
@@ -138,7 +138,7 @@ cn[is.na(CopyNumber), CopyNumber := MajorCN + MinorCN]
## correct copy number beyond maximum CN state based on purity and logR
correctCN <- correctIntegerCN(cn, segs, purity, ploidyT, maxCNtoCorrect.autosomes = NULL,
maxCNtoCorrect.X = NULL, minPurityToCorrect = 0.2, gender = gender, chrs = chrs)
maxCNtoCorrect.X = NULL, minPurityToCorrect = 0.05, gender = gender, chrs = chrs)
segs <- correctCN$segs
cn <- correctCN$cn
## extend segments to remove gaps

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