I have a GRANGES object similar to below:
GRanges object with 3 ranges and 2 metadata columns:
seqnames ranges strand | txid txname
<Rle> <IRanges> <Rle> | <list> <list>
[1] chr1 1-3 + | 1 a
[2] chr1 3-5 - | 2 b
[3] chr1 5-7 + | 1,2 a,b
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
which can be created using
gr <- GRanges(seqnames = "chr1", strand = c("+", "-", "+"),
ranges = IRanges(start = c(1,3,5), width = 3)
)
mcols(gr)$txid <- list(1, 2, list(1, 2))
mcols(gr)$txname <- list("a", "b", list("a", "b"))
and I would like to expand the object so each txid/txname is on a new row, such that the result looks like this:
seqnames ranges strand | txid txname
<Rle> <IRanges> <Rle> | <numeric> <character>
[1] chr1 1-3 + | 1 a
[2] chr1 3-5 - | 2 b
[3] chr1 5-7 + | 1 a
[4] chr1 5-7 + | 2 b
I have tried using S4Vectors::expand() but cannot achieve what I am after.
S4Vectors::expand(gr) expands without consideration for the order of elements in the list. e.g. txid 1 and txname "a" should be on the same row as they are the first elements in their respective lists, and the same goes for txid 2 and txname "b".
The results of S4Vectors::expand(gr) look like this:
seqnames ranges strand | txid txname
<Rle> <IRanges> <Rle> | <numeric> <character>
[1] chr1 1-3 + | 1 a
[2] chr1 3-5 - | 2 b
[3] chr1 5-7 + | 1 a
[4] chr1 5-7 + | 1 b
[5] chr1 5-7 + | 2 a
[6] chr1 5-7 + | 2 b
Expanding just one of the two columns (i.e. S4Vectors::expand(gr, "txid")) works as intended but is not what I'm after:
seqnames ranges strand | txid txname
<Rle> <IRanges> <Rle> | <numeric> <list>
[1] chr1 1-3 + | 1 a
[2] chr1 3-5 - | 2 b
[3] chr1 5-7 + | 1 a,b
[4] chr1 5-7 + | 2 a,b
I feel like I'm close but cannot figure this out on my own so any pointers are welcome. Thank you.
