R/pullOutContent.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 pulls out the relevant contents of the input in res
### Makes it possible for res input to come directly from the segmentation algorithms or winsorize algorithm (regardless of whether res contains only a data frame or a list with segmentation/winsorize results).

## Required by:
### callAberrations
### imputeMissing
### interpolate.pcf
### checkAndRetrievePlotInput
### checkWinsoutliers
### checkSegments
### selectSegments
### subsetSegments
### plotCircle
### plotFreq
### plotHeatmap
### subsetData
### pcf
### pcfPlain
### multipcf
### aspcf


# what could be "segments","estimates","wins.data" or "wins.outliers"

pullOutContent <- function(res, what = "segments") {
  # check if input is data frame or list
  if (!is.data.frame(res)) {
    # res could either be a list containing the two segmentation elements segments and estimates, a list containing the two winsorize elements wins.data and wins.outliers, a list containing several segments as data frames, or a list containing several lists with segmentation results
    if ("segments" %in% names(res)) {
      # can assume that the list contains the output from one of the segmentation algorithms and has names segments and estimates
      # pick out the desired data frame depending on input in what:
      if (what == "estimates") {
        if ("logR_estimates" %in% names(res)) {
          # Segmentation results come from aspcf which returns a different name for estimates
          res <- res$logR_estimates
        } else {
          res <- res$estimates
        }
      } else if (what == "segments") {
        res <- res$segments
      }
    } else if ("wins.data" %in% names(res)) {
      # can assume that the list contains output from winsorize and has names wins.data and wins.outliers
      # pick out the desired data frame depending on input in what:
      if (what %in% c("wins.data", "estimates")) {
        res <- res$wins.data
      } else if (what == "wins.outliers") {
        res <- res$wins.outliers
      }
    } else {
      # assume that the list contains different segmentation results
      # if each element in the list is itself a list containing segments and estimates need to pull out the segments (functions that take estimates as input does not have the option of specifying list of estimates)
      nSeg <- length(res)
      for (l in 1:nSeg) {
        if (!is.data.frame(res[[l]])) {
          # pull out the segments data frame
          res[[l]] <- res[[l]]$segments
        }
      }
    }
  }
  # If a data frame, res should be already be a data frame with the correct information, and does not need modification

  return(res)
}