Nothing
patchwork.Medians_n_AI <- function(segs,kbsegs,alf)
{
## Get medians and AI for them segs
segs$median <- segs$ai <- segs$snvs <- NA
for (i in 1:nrow(segs))
{
ix = kbsegs$chr==as.character(segs$chr[i]) & ( kbsegs$pos > segs$start[i] & kbsegs$pos < segs$end[i] )
segs$median[i] = median(kbsegs$ratio[ix],na.rm=T)
ix2 = alf$achr==as.character(segs$chr[i]) & ( alf$apos > segs$start[i] & alf$apos < segs$end[i] )
segs$snvs[i] = sum(ix2)
segs$ai[i] = 1 - sum(alf$amin[ix2]) / sum(alf$amax[ix2])
#This used for assignAI / updated AI calculation
#segs$ai[i]=median(kbsegs$ai[ix],na.rm=T)
}
segs$ai[is.nan(segs$ai)]=0
segs = segs[!is.na(segs$ai),]
return(segs)
}
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