R/separateChrom.r

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

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## 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
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# Function that returns the index where each chromosome starts (and the last chromosome ends)

## Input:
### v: a vector of chromosome numbers

## Output:
### cp: indeces for start of each chromosome and end of last chromosome

## Required by:
### addChromlines
### adjustSeg

## Requires:
### none


separateChrom <- function(v) {
  d <- diff(v) # get difference between value (i+1) and value i in vector v
  cp <- which(d != 0) + 1 # get changepoints

  # Add start of vector and (stop+1) of the whole vector
  cp <- c(1, cp, (length(v) + 1))

  return(cp)
} # end separateChrom