GInteractions grouping metadata
Usage
# S3 method for class 'GroupedGInteractions'
group_data(.data)
# S3 method for class 'GroupedGInteractions'
group_keys(.tbl, ...)
# S3 method for class 'GroupedGInteractions'
group_indices(.data, ...)
# S3 method for class 'GInteractions'
group_vars(x)
# S3 method for class 'GroupedGInteractions'
group_vars(x)
# S3 method for class 'GroupedGInteractions'
groups(x)
# S3 method for class 'GroupedGInteractions'
group_size(x)
# S3 method for class 'GroupedGInteractions'
n_groups(x)Examples
gi <- read.table(text = "
chr1 11 20 chr1 21 30
chr1 11 20 chr1 51 55
chr1 11 30 chr1 51 55
chr1 11 30 chr2 51 60",
col.names = c(
"seqnames1", "start1", "end1",
"seqnames2", "start2", "end2")
) |>
as_ginteractions() |>
mutate(type = c('cis', 'cis', 'cis', 'trans'), score = runif(4))
ggi <- gi |> group_by(end1)
ggi
#> GroupedGInteractions object with 4 interactions and 2 metadata columns:
#> Groups: end1 [2]
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | type
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 11-20 * --- chr1 21-30 * | cis
#> [2] chr1 11-20 * --- chr1 51-55 * | cis
#> [3] chr1 11-30 * --- chr1 51-55 * | cis
#> [4] chr1 11-30 * --- chr2 51-60 * | trans
#> score
#> <numeric>
#> [1] 0.0652161
#> [2] 0.3542068
#> [3] 0.8251994
#> [4] 0.2738182
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
group_data(ggi)
#> DataFrame with 2 rows and 2 columns
#> end1 .rows
#> <integer> <IntegerList>
#> 1 20 1,2
#> 2 30 3,4
group_keys(ggi)
#> DataFrame with 2 rows and 1 column
#> end1
#> <integer>
#> 1 20
#> 2 30
group_rows(ggi)
#> IntegerList of length 2
#> [[1]] 1 2
#> [[2]] 3 4
group_indices(ggi)
#> integer-Rle of length 4 with 2 runs
#> Lengths: 2 2
#> Values : 1 2
group_vars(ggi)
#> [1] "end1"
groups(ggi)
#> [[1]]
#> end1
#>
group_size(ggi)
#> [1] 2 2
n_groups(ggi)
#> [1] 2