R/interpolate.pcf.r

In igordot/copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

####################################################################
## Author: Gro Nilsen, Knut Liestøl and Ole Christian Lingjærde.
## Maintainer: Gro Nilsen <gronilse@ifi.uio.no>
## License: Artistic 2.0
## Part of the copynumber package
## Reference: Nilsen and Liestøl et al. (2012), BMC Genomics
####################################################################

### Requires:
### pullOutContent

# Function with interpolates pcf-segments
interpolate.pcf <- function(segments, x) {
  # Make sure segments is a data frame
  segments <- pullOutContent(res = segments, what = "segments")

  usamp <- unique(segments$sampleID)
  nsamp <- length(usamp)
  chrom <- unique(x[, 1])
  z <- data.frame(cbind(x[, c(1:2)], matrix(0, nrow(x), nsamp)))
  # z = data.frame(x[,c(1,2)], matrix(0, nrow(x), nsamp))
  names(z) <- c("chr", "pos", usamp)
  for (i in 1:nsamp) {
    for (j in 1:length(chrom)) {
      fitij <- segments[segments$sampleID == usamp[i] & segments$chrom == chrom[j], ]
      v <- (c(fitij$start.pos[-1], 10^9) + fitij$end.pos) / 2
      xj <- x[x[, 1] == chrom[j], 2]
      kj <- rep(0, length(xj))
      for (k in rev(1:length(v))) {
        kj[xj <= v[k]] <- k
      }
      z[z$chr == chrom[j], 2 + i] <- fitij$mean[kj]
    }
  }
  return(z)
}