R/dplyr-select.R
ranges-select.RdSelect metadata columns of the Ranges object by name or position
# S3 method for Ranges
select(.data, ..., .drop_ranges = FALSE)a Ranges object
One or more metadata column names.
If TRUE select will always return a tibble. In this case, you may select columns that form the core part of the Ranges object.
a Ranges object or a tibble
Note that by default select only acts on the metadata columns (and will therefore return a Ranges object) if a core component of a Ranges is dropped or selected without the other required components (this includes the seqnames, strand, start, end, width names), then select will throw an error unless .drop_ranges is set to TRUE.
df <- data.frame(start = 1:10, width = 5, seqnames = "seq1",
strand = sample(c("+", "-", "*"), 10, replace = TRUE), gc = runif(10), counts = rpois(10, 2))
rng <- as_granges(df)
select(rng, -gc)
#> GRanges object with 10 ranges and 1 metadata column:
#> seqnames ranges strand | counts
#> <Rle> <IRanges> <Rle> | <integer>
#> [1] seq1 1-5 * | 2
#> [2] seq1 2-6 * | 1
#> [3] seq1 3-7 + | 5
#> [4] seq1 4-8 - | 1
#> [5] seq1 5-9 * | 1
#> [6] seq1 6-10 - | 4
#> [7] seq1 7-11 - | 2
#> [8] seq1 8-12 + | 1
#> [9] seq1 9-13 + | 2
#> [10] seq1 10-14 + | 1
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
select(rng, gc)
#> GRanges object with 10 ranges and 1 metadata column:
#> seqnames ranges strand | gc
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] seq1 1-5 * | 0.7611217
#> [2] seq1 2-6 * | 0.5733564
#> [3] seq1 3-7 + | 0.4475080
#> [4] seq1 4-8 - | 0.0838020
#> [5] seq1 5-9 * | 0.2191385
#> [6] seq1 6-10 - | 0.0755703
#> [7] seq1 7-11 - | 0.5344268
#> [8] seq1 8-12 + | 0.6413566
#> [9] seq1 9-13 + | 0.5257393
#> [10] seq1 10-14 + | 0.0392814
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
select(rng, counts, gc)
#> GRanges object with 10 ranges and 2 metadata columns:
#> seqnames ranges strand | counts gc
#> <Rle> <IRanges> <Rle> | <integer> <numeric>
#> [1] seq1 1-5 * | 2 0.7611217
#> [2] seq1 2-6 * | 1 0.5733564
#> [3] seq1 3-7 + | 5 0.4475080
#> [4] seq1 4-8 - | 1 0.0838020
#> [5] seq1 5-9 * | 1 0.2191385
#> [6] seq1 6-10 - | 4 0.0755703
#> [7] seq1 7-11 - | 2 0.5344268
#> [8] seq1 8-12 + | 1 0.6413566
#> [9] seq1 9-13 + | 2 0.5257393
#> [10] seq1 10-14 + | 1 0.0392814
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
select(rng, 2:1)
#> GRanges object with 10 ranges and 2 metadata columns:
#> seqnames ranges strand | counts gc
#> <Rle> <IRanges> <Rle> | <integer> <numeric>
#> [1] seq1 1-5 * | 2 0.7611217
#> [2] seq1 2-6 * | 1 0.5733564
#> [3] seq1 3-7 + | 5 0.4475080
#> [4] seq1 4-8 - | 1 0.0838020
#> [5] seq1 5-9 * | 1 0.2191385
#> [6] seq1 6-10 - | 4 0.0755703
#> [7] seq1 7-11 - | 2 0.5344268
#> [8] seq1 8-12 + | 1 0.6413566
#> [9] seq1 9-13 + | 2 0.5257393
#> [10] seq1 10-14 + | 1 0.0392814
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
select(rng, seqnames, strand, .drop_ranges = TRUE)
#> DataFrame with 10 rows and 2 columns
#> seqnames strand
#> <Rle> <Rle>
#> 1 seq1 *
#> 2 seq1 *
#> 3 seq1 +
#> 4 seq1 -
#> 5 seq1 *
#> 6 seq1 -
#> 7 seq1 -
#> 8 seq1 +
#> 9 seq1 +
#> 10 seq1 +