Enhanced GInteractions getters

Usage

anchors1(x)

anchors2(x)

seqnames1(x)

seqnames2(x)

start1(x)

start2(x)

end1(x)

end2(x)

width1(x)

width2(x)

strand1(x)

strand2(x)

ranges1(x)

ranges2(x)

# S4 method for class 'GInteractions'
x$name

# S4 method for class 'GInteractions'
anchors1(x)

# S4 method for class 'GInteractions'
anchors2(x)

# S4 method for class 'GInteractions'
seqnames1(x)

# S4 method for class 'GInteractions'
seqnames2(x)

# S4 method for class 'GInteractions'
start1(x)

# S4 method for class 'GInteractions'
start2(x)

# S4 method for class 'GInteractions'
end1(x)

# S4 method for class 'GInteractions'
end2(x)

# S4 method for class 'GInteractions'
width1(x)

# S4 method for class 'GInteractions'
width2(x)

# S4 method for class 'GInteractions'
strand1(x)

# S4 method for class 'GInteractions'
strand2(x)

# S4 method for class 'GInteractions'
ranges1(x)

# S4 method for class 'GInteractions'
ranges2(x)

Arguments

x: a GInteractions object
name: The pattern or name of a column stored in the GInteractions metadata (mcols).

Value

One of the core GInteractions fields (e.g. seqnames1, start1, ...) or one of the metadata columns when using $. Note that auto-completion works with $.

Examples

gi <- data.frame(
  seqnames1 = 'chr1', start1 = 1, end1 = 10, 
  seqnames2 = 'chr1', start2 = 2, end2 = 20
) |> as_ginteractions() |> mutate(type = 'cis')
anchors1(gi)
#> GRanges object with 1 range and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chr1      1-10      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
anchors2(gi)
#> GRanges object with 1 range and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chr1      2-20      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
seqnames1(gi)
#> factor-Rle of length 1 with 1 run
#>   Lengths:    1
#>   Values : chr1
#> Levels(1): chr1
seqnames2(gi)
#> factor-Rle of length 1 with 1 run
#>   Lengths:    1
#>   Values : chr1
#> Levels(1): chr1
start1(gi)
#> [1] 1
start2(gi)
#> [1] 2
end1(gi)
#> [1] 10
end2(gi)
#> [1] 20
width1(gi)
#> [1] 10
width2(gi)
#> [1] 19
ranges1(gi)
#> IRanges object with 1 range and 0 metadata columns:
#>           start       end     width
#>       <integer> <integer> <integer>
#>   [1]         1        10        10
ranges2(gi)
#> IRanges object with 1 range and 0 metadata columns:
#>           start       end     width
#>       <integer> <integer> <integer>
#>   [1]         2        20        19
strand1(gi)
#> factor-Rle of length 1 with 1 run
#>   Lengths: 1
#>   Values : *
#> Levels(3): + - *
strand2(gi)
#> factor-Rle of length 1 with 1 run
#>   Lengths: 1
#>   Values : *
#> Levels(3): + - *
gi$type
#> [1] "cis"