Group GInteractions by columns
Value
a GroupedGInteractions object. When a
(Anchored)PinnedGInteractions object is grouped, both anchoring and
pinning are dropped.
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))
####################################################################
# 1. Group by core column
####################################################################
gi |> group_by(end1)
#> 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] 0.9805397
#> [2] 0.7415215
#> [3] 0.0514463
#> [4] 0.5302125
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |> group_by(end1, end2) |> group_data()
#> DataFrame with 4 rows and 3 columns
#> end1 end2 .rows
#> <integer> <integer> <IntegerList>
#> 1 20 30 1
#> 2 20 55 2
#> 3 30 55 3
#> 4 30 60 4
####################################################################
# 2. Group by metadata column
####################################################################
gi |> group_by(type) |> group_data()
#> DataFrame with 2 rows and 2 columns
#> type .rows
#> <character> <IntegerList>
#> 1 cis 1,2,3
#> 2 trans 4
####################################################################
# 3. Combine core and metadata column grouping
####################################################################
gi |> group_by(end1, type)
#> GroupedGInteractions object with 4 interactions and 2 metadata columns:
#> Groups: end1, type [3]
#> 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] 0.9805397
#> [2] 0.7415215
#> [3] 0.0514463
#> [4] 0.5302125
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |> group_by(end1, type) |> group_data()
#> DataFrame with 3 rows and 3 columns
#> end1 type .rows
#> <integer> <character> <IntegerList>
#> 1 20 cis 1,2
#> 2 30 cis 3
#> 3 30 trans 4
####################################################################
# 4. Create a new column and group by this new variable
####################################################################
gi |> group_by(class = c(1, 2, 1, 2))
#> GroupedGInteractions object with 4 interactions and 3 metadata columns:
#> Groups: class [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 class
#> <numeric> <numeric>
#> [1] 0.9805397 1
#> [2] 0.7415215 2
#> [3] 0.0514463 1
#> [4] 0.5302125 2
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
####################################################################
# 5. Replace or add groups to a GroupedGInteractions
####################################################################
ggi <- gi |> group_by(class = c(1, 2, 1, 2))
ggi |> group_data()
#> DataFrame with 2 rows and 2 columns
#> class .rows
#> <numeric> <IntegerList>
#> 1 1 1,3
#> 2 2 2,4
ggi |> group_by(type) |> group_data()
#> DataFrame with 2 rows and 2 columns
#> type .rows
#> <character> <IntegerList>
#> 1 cis 1,2,3
#> 2 trans 4
ggi |> group_by(type, .add = TRUE) |> group_data()
#> DataFrame with 3 rows and 3 columns
#> class type .rows
#> <numeric> <character> <IntegerList>
#> 1 1 cis 1,3
#> 2 2 cis 2
#> 3 2 trans 4
####################################################################
# 6. Ungroup GInteractions
####################################################################
ggi <- gi |> group_by(type, class = c(1, 2, 1, 2))
ggi
#> GroupedGInteractions object with 4 interactions and 3 metadata columns:
#> Groups: type, class [3]
#> 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 class
#> <numeric> <numeric>
#> [1] 0.9805397 1
#> [2] 0.7415215 2
#> [3] 0.0514463 1
#> [4] 0.5302125 2
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
ungroup(ggi, type)
#> GroupedGInteractions object with 4 interactions and 3 metadata columns:
#> Groups: class [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 class
#> <numeric> <numeric>
#> [1] 0.9805397 1
#> [2] 0.7415215 2
#> [3] 0.0514463 1
#> [4] 0.5302125 2
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
ungroup(ggi, class)
#> GroupedGInteractions object with 4 interactions and 3 metadata columns:
#> Groups: type [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 class
#> <numeric> <numeric>
#> [1] 0.9805397 1
#> [2] 0.7415215 2
#> [3] 0.0514463 1
#> [4] 0.5302125 2
#> -------
#> regions: 5 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths