Expand list-columns in a Ranges object
expand_ranges(
data,
...,
.drop = FALSE,
.id = NULL,
.keep_empty = FALSE,
.recursive = FALSE
)A Ranges object
list-column names to expand then unlist
Should additional list columns be dropped (default = FALSE)?
By default expand_ranges() will keep other list columns even if they are nested.
A character vector of length equal to number of list columns.
If supplied will create new column(s) with name .id
identifying the index of the list column (default = NULL).
If a list-like column contains empty elements, should those elements be kept? (default = FALSE)
If there are multiple list-columns, should the columns be treated as parallel? If FALSE each column will be unnested recursively, otherwise they are treated as parallel, that is each list column has identical lengths. (deafualt = FALSE)
a GRanges object with expanded list columns
grng <- as_granges(data.frame(seqnames = "chr1", start = 20:23, width = 1000))
grng <- mutate(grng,
exon_id = IntegerList(a = 1, b = c(4,5), c = 3, d = c(2,5))
)
expand_ranges(grng)
#> GRanges object with 6 ranges and 1 metadata column:
#> seqnames ranges strand | exon_id
#> <Rle> <IRanges> <Rle> | <integer>
#> [1] chr1 20-1019 * | 1
#> [2] chr1 21-1020 * | 4
#> [3] chr1 21-1020 * | 5
#> [4] chr1 22-1021 * | 3
#> [5] chr1 23-1022 * | 2
#> [6] chr1 23-1022 * | 5
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
expand_ranges(grng, .id = "name")
#> GRanges object with 6 ranges and 2 metadata columns:
#> seqnames ranges strand | exon_id name
#> <Rle> <IRanges> <Rle> | <integer> <character>
#> [1] chr1 20-1019 * | 1 a
#> [2] chr1 21-1020 * | 4 b
#> [3] chr1 21-1020 * | 5 b
#> [4] chr1 22-1021 * | 3 c
#> [5] chr1 23-1022 * | 2 d
#> [6] chr1 23-1022 * | 5 d
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# empty list elements are not preserved by default
grng <- mutate(grng,
exon_id = IntegerList(a = NULL, b = c(4,5), c= 3, d = c(2,5))
)
expand_ranges(grng)
#> GRanges object with 5 ranges and 1 metadata column:
#> seqnames ranges strand | exon_id
#> <Rle> <IRanges> <Rle> | <integer>
#> [1] chr1 21-1020 * | 4
#> [2] chr1 21-1020 * | 5
#> [3] chr1 22-1021 * | 3
#> [4] chr1 23-1022 * | 2
#> [5] chr1 23-1022 * | 5
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
expand_ranges(grng, .keep_empty = TRUE)
#> GRanges object with 6 ranges and 1 metadata column:
#> seqnames ranges strand | exon_id
#> <Rle> <IRanges> <Rle> | <integer>
#> [1] chr1 20-1019 * | <NA>
#> [2] chr1 21-1020 * | 4
#> [3] chr1 21-1020 * | 5
#> [4] chr1 22-1021 * | 3
#> [5] chr1 23-1022 * | 2
#> [6] chr1 23-1022 * | 5
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
expand_ranges(grng, .id = "name", .keep_empty = TRUE)
#> GRanges object with 6 ranges and 2 metadata columns:
#> seqnames ranges strand | exon_id name
#> <Rle> <IRanges> <Rle> | <integer> <character>
#> [1] chr1 20-1019 * | <NA> a
#> [2] chr1 21-1020 * | 4 b
#> [3] chr1 21-1020 * | 5 b
#> [4] chr1 22-1021 * | 3 c
#> [5] chr1 23-1022 * | 2 d
#> [6] chr1 23-1022 * | 5 d
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths