Description Usage Arguments Details Value
Score chromosomal level copy number changes.
1 2 3 4 5 6 |
segFiles |
String or vector of strings. Path to segment files. |
threshLow |
Numeric. Threshold above which to call copy number gain or loss. |
threshHigh |
Numeric. Threshold above which to call extreme copy numebr gain or loss. |
doRel |
Boolean. Whether to adjust scores based on relative lengths of chromosomes. |
doCat |
Boolean. Whether to categorise copy number chaanges into chromosomal, arm-level, focal or large split. |
doScale |
Boolean. Whether to scale copy number scores. |
tumTotCol |
Integer. Seg column with total copy number information for tumour sample. |
normTotCol |
Integer. Seg column with total copy number information for matched normal sample. |
startCol |
Integer. Seg column with segment start positions. |
endCol |
Integer. Seg column with segment end positions. |
chromCol |
Integer. Seg column with segment chromosomes. |
sampleCol |
Integer. Seg column with sample names for each segment. |
head |
Boolean. Whether seg file has headers. |
Implements copy number scores from Davoli et al. (2017).
Matrix of copy number categories if doCat=TRUE
, or vector of copy number scores if doCat=FALSE
.
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