[Bioc-devel] Collapsing a GRangesList into a GRanges without loosing names(GRangesList)

[Shepherd, Lori]

In what way are you feeling they loose names?

> grlist <- GenomicRanges::GRangesList( gr1 = GenomicRanges::GRanges('chr1', '1-100',   strand = '-'), gr2 = GenomicRanges::GRanges('chr1', '101-200', strand = '-'))

> names(grlist)
[1] "gr1" "gr2"

> temp = unlist(grlist)
> names(temp)
[1] "gr1" "gr2"

> temp
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  gr1     chr1     1-100      -
  gr2     chr1   101-200      -
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

> temp["gr1"]
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  gr1     chr1     1-100      -
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths



The names "gr1" and "gr2"  were preserved. You can see them as the first entry in my temp object.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Bhagwat, Aditya <Aditya.Bhagwat using mpi-bn.mpg.de>
Sent: Wednesday, September 11, 2019 8:47 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Collapsing a GRangesList into a GRanges without loosing names(GRangesList)

Dear bioc-devel,

When using unlist to collapse a GRangesList into a GRanges<https://support.bioconductor.org/p/83599>  one looses names(GRangesList).
Since I need a name-preserving collapser, I defined the following in multicrispr<https://gitlab.gwdg.de/loosolab/software/multicrispr>.
My feedback request is: did I overlook existing similar functionality?

#' Collapse a GRangesList
#' @param grangeslist GenomicRanges::GRangesList
#' @examples
#' # Consider a GRangesList
#'     grlist <- GenomicRanges::GRangesList(
#'         gr1 = GenomicRanges::GRanges('chr1', '1-100',   strand = '-'),
#'         gr2 = GenomicRanges::GRanges('chr1', '101-200', strand = '-'))
#'
#' # unlist() drops names(grlist)
#'     unlist(grlist)
#'
#' # collapse() preserves them
#'     collapse(grlist)
#'
#' # in a way similar to as.data.frame()
#'     as.data.frame(grlist)
#' @export
collapse <- function(grangeslist){
    add_series <- function(granges, group_name){
                    granges$group_name <- group_name;
                    granges }
    S4Vectors::mendoapply(add_series, grangeslist, names(grangeslist)) %>%
    unlist() %>%
    sort()
}


Aditya

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