Mutate columns from a GInteractions object
Usage
# S3 method for class 'GInteractions'
mutate(.data, ...)
# S3 method for class 'GroupedGInteractions'
mutate(.data, ...)Examples
gi <- read.table(text = "
chr1 10 20 chr1 50 51
chr1 10 50 chr2 30 40",
col.names = c("chr1", "start1", "end1", "chr2", "start2", "end2")) |>
as_ginteractions(seqnames1 = chr1, seqnames2 = chr2)
####################################################################
# 1. Add metadata columns to a GInteractions object
####################################################################
gi |>
mutate(type = c('cis', 'trans'), score = runif(2)) |>
mutate(type2 = type)
#> GInteractions object with 2 interactions and 3 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | type
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 10-20 * --- chr1 50-51 * | cis
#> [2] chr1 10-50 * --- chr2 30-40 * | trans
#> score type2
#> <numeric> <character>
#> [1] 0.695824 cis
#> [2] 0.688556 trans
#> -------
#> regions: 4 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
####################################################################
# 2. More complex, nested or inplace changes
####################################################################
gi |>
mutate(type = c('cis', 'trans'), score = runif(2)) |>
mutate(type2 = type) |>
mutate(count = c(1, 2), score = count * 2, new_col = paste0(type2, score))
#> GInteractions object with 2 interactions and 5 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | type
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 10-20 * --- chr1 50-51 * | cis
#> [2] chr1 10-50 * --- chr2 30-40 * | trans
#> score type2 count new_col
#> <numeric> <character> <numeric> <character>
#> [1] 2 cis 1 cis2
#> [2] 4 trans 2 trans4
#> -------
#> regions: 4 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
####################################################################
# 3. Core GInteractions columns can also be modified
####################################################################
gi |>
mutate(start1 = 1, end1 = 10, width2 = 30, strand2 = c('-', '+'))
#> GInteractions object with 2 interactions and 0 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle>
#> [1] chr1 1-10 * --- chr1 50-79 -
#> [2] chr1 1-10 * --- chr2 30-59 +
#> -------
#> regions: 3 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
# Note how the core columns are modified sequentially
gi |>
mutate(start1 = 1, end1 = 10)
#> GInteractions object with 2 interactions and 0 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle>
#> [1] chr1 1-10 * --- chr1 50-51 *
#> [2] chr1 1-10 * --- chr2 30-40 *
#> -------
#> regions: 3 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
gi |>
mutate(start1 = 1, end1 = 10, width1 = 50)
#> GInteractions object with 2 interactions and 0 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle>
#> [1] chr1 1-50 * --- chr1 50-51 *
#> [2] chr1 1-50 * --- chr2 30-40 *
#> -------
#> regions: 3 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
####################################################################
# 4. Evaluating core GInteractions columns
####################################################################
gi |>
mutate(
score = runif(2),
cis = seqnames1 == seqnames2,
distance = ifelse(cis, start2 - end1, NA)
)
#> GInteractions object with 2 interactions and 3 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 10-20 * --- chr1 50-51 * | 0.300831
#> [2] chr1 10-50 * --- chr2 30-40 * | 0.636466
#> cis distance
#> <Rle> <integer>
#> [1] TRUE 30
#> [2] FALSE <NA>
#> -------
#> regions: 4 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
####################################################################
# 5. Grouped GInteractions are modified group by group
####################################################################
gi4 <- read.table(text = "
chr1 10 20 chr1 50 51
chr1 10 50 chr2 30 40
chr1 30 40 chr1 60 70
chr1 30 40 chr2 20 25",
col.names = c("chr1", "start1", "end1", "chr2", "start2", "end2")) |>
as_ginteractions(seqnames1 = chr1, seqnames2 = chr2) |>
mutate(score = c(1, 2, 3, 6))
gi4 |>
group_by(seqnames2) |>
mutate(mean_score = mean(score), start1 = start1 + 1)
#> GroupedGInteractions object with 4 interactions and 2 metadata columns:
#> Groups: seqnames2 [2]
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr1 11-20 * --- chr1 50-51 * | 1
#> [2] chr1 11-50 * --- chr2 30-40 * | 2
#> [3] chr1 31-40 * --- chr1 60-70 * | 3
#> [4] chr1 31-40 * --- chr2 20-25 * | 6
#> mean_score
#> <numeric>
#> [1] 2
#> [2] 4
#> [3] 2
#> [4] 4
#> -------
#> regions: 7 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths