R/get.seglim.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
####################################################################

# Function that finds the y-range of segments to be plotted

# Input:
### segments: dataframe with a segmentation result
### equalRange: should range be found over all samples and chromosomes in segments?
### sampleID: a sampleID for which range is to be found
### chrom: a chromosome number for which range is to be found
### baf: are we looking for range of baf-segments? if so; these values are found in column 8, otherwise they are found in column 7

# Output:
### seg.lim: vector of length 2 giving the minimum and maximum segment limit

## Required by:
### plotAllele
### plotChrom
### plotGenome
### plotSample



## Requires:
### none

get.seglim <- function(segments, equalRange, sampleID = NULL, k = NULL, baf = FALSE) {
  if (equalRange) {
    # Use all segments to determine limits:
    use.segments <- segments
  } else {
    # Use only segments indicated by index or k to calculate limits:
    if (!is.null(k)) {
      use.segments <- segments[segments[, 2] == k, ]
    } else {
      if (!is.null(sampleID)) {
        keep <- which(segments[, 1] == sampleID)
        use.segments <- segments[keep, ]
      }
    }
  }
  seg.lim <- rep(NA, 2)

  if (nrow(use.segments) > 0) {
    if (!baf) {
      seg.lim <- c(min(use.segments[, 7]), max(use.segments[, 7]))
    } else {
      seg.lim <- c(min(use.segments[, 8]), max(use.segments[, 8]))
    }
  }

  return(seg.lim)
} # end get.seglim