8000 CNA data extract missing X & Y · Issue #5 · zhandong/TCGA2STAT · GitHub
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CNA data extract missing X & Y #5

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nknowlton 6FFD opened this issue Aug 27, 2017 · 0 comments
Open

CNA data extract missing X & Y #5

nknowlton opened this issue Aug 27, 2017 · 0 comments

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@nknowlton
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The GetSegments.ByGene function performs a mapping of X & Y against the TCGA data. TCGA stores X as 23 and Y as 24, so no mapping of these chromosomes is possible. A fix is to simply add

dat$chrom[dat$chrom == 23]<-"X"
dat$chrom[dat$chrom == 24]<-"Y"

After the filter.
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