callAlterations {PureCN} | R Documentation |
Function to extract major copy number alterations from a
runAbsoluteCN
return object.
callAlterations(res, id = 1, cutoffs = c(0.5, 6, 7), log.ratio.cutoffs = c(-0.9, 0.9), failed = NULL, all.genes = FALSE)
res |
Return object of the |
id |
Candidate solutions to be used. |
cutoffs |
Copy numbers cutoffs to call losses, focal amplifications and broad amplifications. |
log.ratio.cutoffs |
Copy numbers log-ratio cutoffs to call losses and amplifications in failed samples. |
failed |
Indicates whether sample was failed. If |
all.genes |
If |
A data.frame
with gene-level amplification and deletion
calls.
Markus Riester
data(purecn.example.output) callAlterations(purecn.example.output) callAlterations(purecn.example.output, all.genes=TRUE)["ESR2",]