R/checkChrom.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 to check that specified chrom are numeric, found in data and/or segments and print appropriate error/warning messages depending on the plot type
# If chrom=NULL; all unique chromosomes found in data and/or segments are selected

# Input:
### chrom: a vector of unique chromosome numbers, or NULL
### data: the copy number data frame
### segments: a list containing one or more segmentations
### type: plot type (sample,chromosome,aspcf)


## Output:
### use.chrom : a vector of unique selected chromosomes to be plotted

## Function called by:
### plotFreq
### plotHeatmap
### plotWeightedFreq
### checkAndRetrievePlotInput

## Function calls:
### numericChrom

checkChrom <- function(data, segments, chrom) {
  chrom.list <- NULL

  if (!is.null(data)) {
    chrom.list <- unique(data[, 1])
  }
  if (!is.null(segments)) {
    all.chrom <- sapply(segments, "[", i = 2) # returns a list with chromsome numbers for each segmentation
    seg.chrom <- lapply(all.chrom, unique)


    # Find common chromosomes in data and all segmentations:
    i <- 1
    if (is.null(chrom.list)) {
      chrom.list <- seg.chrom[[1]]
      i <- i + 1
    }
    while (i <= length(seg.chrom)) {
      chrom.list <- intersect(chrom.list, seg.chrom[[i]])
      i <- i + 1
    }
  } # endif

  # Check input chromosomes, print error or warning if needed:
  if (is.null(chrom)) {
    use.chrom <- chrom.list
  } else {
    # Make sure chrom is numeric
    chrom <- numericChrom(chrom)

    # Check that specified chrom are all in allowed list (found in data and segments):
    use <- chrom %in% chrom.list
    use.chrom <- chrom[use]
    if (length(use.chrom) == 0) {
      # print error message
      if (!is.null(data) && !is.null(segments)) {
        msg <- "Specified chromosome(s) are not found in data and/or segments"
      } else if (is.null(segments)) {
        msg <- "Specified chromosome(s) are not found in data"
      } else {
        msg <- "Specified chromosome(s) are not found in segments"
      }
      stop(msg, call. = FALSE)
    } else if (length(use.chrom) != length(chrom)) {
      not.use <- paste(chrom[!use], sep = "", collapse = ",")
      if (!is.null(data) && !is.null(segments)) {
        msg <- "The following chromosome(s) are not found in data and/or segments:"
      } else if (is.null(segments)) {
        msg <- "The following chromosome(s) are not found in data:"
      } else {
        msg <- "The following chromosome(s) are not found in segments:"
      }
      warning(paste(msg, not.use, sep = " "), call. = FALSE, immediate. = TRUE)
    }
  } # endif

  # make sure that chromosome numbers are in increasing order
  use.chrom <- sort(use.chrom)

  return(use.chrom)
} # end checkChrom