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-boun...@r-project.org> on behalf of Bhagwat,
Aditya <aditya.bhag...@mpi-bn.mpg.de>
Sent: Wednesday, September 11, 2019 8:47 AM
To: bioc-devel@r-project.org <bioc-devel@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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