Hello,

I was surprised to observe two unexpected clear peaks at 0 and 5 in the raw copy numbers distribution, so I looked at the code and found this:

setMethod("CA", signature=signature(object="CNSet"),
function(object, ...){
ca <- ACN(object, allele="A", ...)
ca[ca < 0] <- 0
ca[ca > 5] <- 5
return(ca)
})
setMethod("CB", signature=signature(object="CNSet"),
function(object, ...) {
cb <- ACN(object, allele="B", ...)
cb[cb < 0] <- 0
cb[cb > 5] <- 5
return(cb)
})
setMethod("totalCopynumber", signature=signature(object="CNSet"),
function(object, ...){
ca <- CA(object, ...)
cb <- CB(object, ...)
return(ca+cb)
})
rawCopynumber <- totalCopynumber

This means that the copy numbers are indeed explicitly forced in the [0-5] range.

My question being: why ?

Best regards,

Karl Forner