Description Usage Arguments Value Author(s) Examples
Somatic copy number corrected by admixture rate.
1 | copynumberCorrected(segment, admix)
|
segment |
A GRanges class, segments with annotation of somatic ratio. |
admix |
Numeric. Admixture rate of normal cells. |
A GRanges class, segments with annotation of event.
seqnames, ranges |
See GRanges(). |
medLAF |
A numeric vector. Median lesser allele frequency of each segment in the tumor sample. |
ratio |
A numeric vector. Somatic ratio (read depth ratio of tumor/normal) of each segment. |
somaCN |
An integer vector. Somatic integer copy number based on somatic ratio. |
event |
A character vector. Somatic event characterization based on somatic ratio, taking values of "=", "Loss", "Gain", "LOH", "neutral LOH" or "double deletion". |
Mengjie Chen
1 2 3 4 5 6 7 8 9 10 | data(segwithratio)
x <- GRanges(seqnames=segwithratio$chromosome,
ranges=IRanges(start=segwithratio$start,
end=segwithratio$end),
medLAF=segwithratio$medLAF,
medgLAF=segwithratio$medgermlineLAF,
ratio=segwithratio$ratio
)
admix <- 0.4
y <- copynumberCorrected(x, admix)
|
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