R/checkSegments.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 checks and modfies the input provided in segments in plot functions

## Input:
### segments: data frame or list with data frames containing segmentation results
### type: plot type

## Output:
### new.segments: Checked and modified list of segments

## Required by:
### checkAndRetrievePlotInput


## Requires:
### getUnisegFormat
### is.multiseg
### numericChrom
### pullOutContent


checkSegments <- function(segments, type) {
  # Check and pull out relevant information in segments
  segments <- pullOutContent(res = segments, what = "segments")

  # Get on list form if segments is matrix or data frame:
  if (class(segments) != "list") {
    segments <- list(seg = segments)
  }

  nSeg <- length(segments)
  seg.names <- names(segments)
  if (is.null(seg.names)) {
    seg.names <- paste("Seg", 1:nSeg, "")
  }
  # Segments could be on uniseg or multiseg form, convert all to uniseg form:
  new.segments <- vector("list", nSeg) # empty list
  for (s in 1:nSeg) {
    use.seg <- segments[[s]]
    multi <- is.multiseg(use.seg)
    if (multi) {
      # stopifnot(ncol(use.seg)>=6)
      if (ncol(use.seg) < 6) {
        stop("segments format is not correct", call. = FALSE)
      }
      # Convert to uniseg format:
      use.seg <- getUnisegFormat(use.seg)
    } else {
      if (type != "aspcf") {
        if (ncol(use.seg) < 7) {
          stop("segments format is not correct", call. = FALSE)
          # stopifnot(ncol(use.seg)>=7)
        }
      } else {
        if (ncol(use.seg) < 8) {
          stop("segments format is not correct", call. = FALSE)
        }
      }
    }
    # Make sure chromosomes in column 2 are numeric:
    use.seg[, 2] <- numericChrom(use.seg[, 2])
    # Make sure arms in column 3 are character:
    use.seg[, 3] <- as.character(use.seg[, 3])

    new.segments[[s]] <- use.seg
  }

  names(new.segments) <- seg.names

  return(new.segments)
} # end checkSegments