Choose rows by their position
a Ranges object
Integer row values indicating rows to keep. If .data has
been grouped via group_by(), then the positions are selected within each group.
when FALSE (the default) the grouping structure is recomputed, otherwise it is kept as is. Currently ignored.
a GRanges object
df <- data.frame(start = 1:10,
width = 5,
seqnames = "seq1",
strand = sample(c("+", "-", "*"), 10, replace = TRUE),
gc = runif(10))
rng <- as_granges(df)
dplyr::slice(rng, 1:2)
#> GRanges object with 2 ranges and 1 metadata column:
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 1-5 - | 0.792625
#> [2] seq1 2-6 - | 0.614470
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
dplyr::slice(rng, -n())
#> GRanges object with 9 ranges and 1 metadata column:
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 1-5 - | 0.792625
#> [2] seq1 2-6 - | 0.614470
#> [3] seq1 3-7 - | 0.700621
#> [4] seq1 4-8 - | 0.107933
#> [5] seq1 5-9 * | 0.333866
#> [6] seq1 6-10 + | 0.324132
#> [7] seq1 7-11 * | 0.565426
#> [8] seq1 8-12 + | 0.203178
#> [9] seq1 9-13 + | 0.219705
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
dplyr::slice(rng, -5:-n())
#> GRanges object with 4 ranges and 1 metadata column:
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 1-5 - | 0.792625
#> [2] seq1 2-6 - | 0.614470
#> [3] seq1 3-7 - | 0.700621
#> [4] seq1 4-8 - | 0.107933
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
by_strand <- group_by(rng, strand)
# slice with group by finds positions within each group
dplyr::slice(by_strand, n())
#> GRanges object with 3 ranges and 1 metadata column:
#> Groups: strand [3]
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 7-11 * | 0.565426
#> [2] seq1 9-13 + | 0.219705
#> [3] seq1 10-14 - | 0.633115
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
dplyr::slice(by_strand, which.max(gc))
#> GRanges object with 3 ranges and 1 metadata column:
#> Groups: strand [3]
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 1-5 - | 0.792625
#> [2] seq1 6-10 + | 0.324132
#> [3] seq1 7-11 * | 0.565426
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# if the index is beyond the number of groups slice are ignored
dplyr::slice(by_strand, 1:3)
#> GRanges object with 8 ranges and 1 metadata column:
#> Groups: strand [3]
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 1-5 - | 0.792625
#> [2] seq1 2-6 - | 0.614470
#> [3] seq1 3-7 - | 0.700621
#> [4] seq1 5-9 * | 0.333866
#> [5] seq1 6-10 + | 0.324132
#> [6] seq1 7-11 * | 0.565426
#> [7] seq1 8-12 + | 0.203178
#> [8] seq1 9-13 + | 0.219705
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths