Nothing
seg.summary <-
function (data, segs, chr)
{
cnv <- as.data.frame(matrix(NA,nrow(segs),15))
names(cnv) <- c("chr","posStart","posEnd","length","chrIdxStart","chrIdxEnd","numProbe",
"log2ratio.Mean","log2ratio.SD","log2ratio.Median","log2ratio.MAD",
"log2mBAF.Mean","log2mBAF.SD","log2mBAF.Median","log2mBAF.MAD")
for (i in 1:nrow(segs)) {
idx.start <- segs[i,1]; idx.end <- segs[i,2]
idx <- idx.start:idx.end
start <- data$pos[idx.start]; end <- data$pos[idx.end]
## seg info
cnv$chr[i] <- chr
cnv$posStart[i] <- start
cnv$posEnd[i] <- end
cnv$length[i] <- end - start + 1
cnv$chrIdxStart[i] <- idx.start
cnv$chrIdxEnd[i] <- idx.end
cnv$numProbe[i] <- length(idx)
## statistics
cnv$log2ratio.Mean[i] <- mean(data$log2ratio[idx],na.rm=T)
cnv$log2ratio.SD[i] <- sd(data$log2ratio[idx],na.rm=T)
cnv$log2ratio.Median[i] <- median(data$log2ratio[idx],na.rm=T)
cnv$log2ratio.MAD[i] <- mad(data$log2ratio[idx],na.rm=T)
cnv$log2mBAF.Mean[i] <- mean(data$log2mBAF[idx],na.rm=T)
cnv$log2mBAF.SD[i] <- sd(data$log2mBAF[idx],na.rm=T)
cnv$log2mBAF.Median[i] <- median(data$log2mBAF[idx],na.rm=T)
cnv$log2mBAF.MAD[i] <- mad(data$log2mBAF[idx],na.rm=T)
}
return(cnv)
}
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