Select columns within GInteractions metadata columns
Usage
# S3 method for class 'GInteractions'
select(.data, ..., .drop_ranges = FALSE)Examples
gi <- read.table(text = "
chr1 1 10 chr1 1 10
chr2 1 10 chr2 1 10
chr3 1 10 chr3 1 10
chr4 1 10 chr4 1 10
chr5 1 10 chr5 1 10",
col.names = c(
"seqnames1", "start1", "end1",
"seqnames2", "start2", "end2")
) |>
as_ginteractions() |>
mutate(score = runif(5)*100, cis = TRUE, gc = runif(5))
####################################################################
# 1. Select metadata columns from GInteractions by index
####################################################################
gi |> select(2, 1)
#> GInteractions object with 5 interactions and 2 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | cis
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <logical>
#> [1] chr1 1-10 * --- chr1 1-10 * | TRUE
#> [2] chr2 1-10 * --- chr2 1-10 * | TRUE
#> [3] chr3 1-10 * --- chr3 1-10 * | TRUE
#> [4] chr4 1-10 * --- chr4 1-10 * | TRUE
#> [5] chr5 1-10 * --- chr5 1-10 * | TRUE
#> score
#> <numeric>
#> [1] 70.6434
#> [2] 94.8577
#> [3] 18.0339
#> [4] 21.6900
#> [5] 68.0163
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
gi |> select(-3)
#> GInteractions object with 5 interactions and 2 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 1-10 * --- chr1 1-10 * | 70.6434
#> [2] chr2 1-10 * --- chr2 1-10 * | 94.8577
#> [3] chr3 1-10 * --- chr3 1-10 * | 18.0339
#> [4] chr4 1-10 * --- chr4 1-10 * | 21.6900
#> [5] chr5 1-10 * --- chr5 1-10 * | 68.0163
#> cis
#> <logical>
#> [1] TRUE
#> [2] TRUE
#> [3] TRUE
#> [4] TRUE
#> [5] TRUE
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
####################################################################
# 2. Select metadata columns from GInteractions by name
####################################################################
gi |> select(gc, score)
#> GInteractions object with 5 interactions and 2 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | gc
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 1-10 * --- chr1 1-10 * | 0.4988456
#> [2] chr2 1-10 * --- chr2 1-10 * | 0.6416793
#> [3] chr3 1-10 * --- chr3 1-10 * | 0.6602843
#> [4] chr4 1-10 * --- chr4 1-10 * | 0.0960242
#> [5] chr5 1-10 * --- chr5 1-10 * | 0.7656002
#> score
#> <numeric>
#> [1] 70.6434
#> [2] 94.8577
#> [3] 18.0339
#> [4] 21.6900
#> [5] 68.0163
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
####################################################################
# 3. Select metadata columns from GInteractions with <tidy-select>
####################################################################
gi |> select(contains('s'))
#> GInteractions object with 5 interactions and 2 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 1-10 * --- chr1 1-10 * | 70.6434
#> [2] chr2 1-10 * --- chr2 1-10 * | 94.8577
#> [3] chr3 1-10 * --- chr3 1-10 * | 18.0339
#> [4] chr4 1-10 * --- chr4 1-10 * | 21.6900
#> [5] chr5 1-10 * --- chr5 1-10 * | 68.0163
#> cis
#> <logical>
#> [1] TRUE
#> [2] TRUE
#> [3] TRUE
#> [4] TRUE
#> [5] TRUE
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
gi |> select(matches('^s'))
#> GInteractions object with 5 interactions and 1 metadata column:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 1-10 * --- chr1 1-10 * | 70.6434
#> [2] chr2 1-10 * --- chr2 1-10 * | 94.8577
#> [3] chr3 1-10 * --- chr3 1-10 * | 18.0339
#> [4] chr4 1-10 * --- chr4 1-10 * | 21.6900
#> [5] chr5 1-10 * --- chr5 1-10 * | 68.0163
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
####################################################################
# 4. Select core and metadata columns with .drop_ranges = TRUE
####################################################################
gi |> select(matches('^s'), .drop_ranges = TRUE)
#> DataFrame with 5 rows and 7 columns
#> seqnames1 start1 strand1 seqnames2 start2 strand2 score
#> <Rle> <integer> <Rle> <Rle> <integer> <Rle> <numeric>
#> 1 chr1 1 * chr1 1 * 70.6434
#> 2 chr2 1 * chr2 1 * 94.8577
#> 3 chr3 1 * chr3 1 * 18.0339
#> 4 chr4 1 * chr4 1 * 21.6900
#> 5 chr5 1 * chr5 1 * 68.0163