Why are the raw copy numbers maxed at 5 and minned at 0 ?
0
0
Entering edit mode
kforner • 0
@kforner-7188
Last seen 6.5 years ago
Switzerland

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

 

 

 

 

crlmm copy number • 596 views
ADD COMMENT

Login before adding your answer.

Traffic: 254 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6