Subset a GInteractions with tidyverse-like filter
Usage
# S3 method for class 'GInteractions'
filter(.data, ...)Examples
gi <- read.table(text = "
chr1 1 10 chr1 1 10
chr1 2 10 chr2 1 10
chr3 3 10 chr3 1 10
chr4 4 10 chr4 1 10
chr5 5 10 chr5 1 10",
col.names = c(
"seqnames1", "start1", "end1",
"seqnames2", "start2", "end2")
) |>
as_ginteractions() |>
mutate(cis = seqnames1 == seqnames2, score = runif(5)*100, gc = runif(5))
gi
#> GInteractions object with 5 interactions and 3 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | cis
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <Rle>
#> [1] chr1 1-10 * --- chr1 1-10 * | TRUE
#> [2] chr1 2-10 * --- chr2 1-10 * | FALSE
#> [3] chr3 3-10 * --- chr3 1-10 * | TRUE
#> [4] chr4 4-10 * --- chr4 1-10 * | TRUE
#> [5] chr5 5-10 * --- chr5 1-10 * | TRUE
#> score gc
#> <numeric> <numeric>
#> [1] 73.53196 0.5302125
#> [2] 19.59567 0.6958239
#> [3] 98.05397 0.6885560
#> [4] 74.15215 0.0312303
#> [5] 5.14463 0.2255625
#> -------
#> regions: 9 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
####################################################################
# 1. Filter metadata columns from GInteractions by condition
####################################################################
gi |> filter(gc > 0.1)
#> GInteractions object with 4 interactions and 3 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | cis
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <Rle>
#> [1] chr1 1-10 * --- chr1 1-10 * | TRUE
#> [2] chr1 2-10 * --- chr2 1-10 * | FALSE
#> [3] chr3 3-10 * --- chr3 1-10 * | TRUE
#> [4] chr5 5-10 * --- chr5 1-10 * | TRUE
#> score gc
#> <numeric> <numeric>
#> [1] 73.53196 0.530212
#> [2] 19.59567 0.695824
#> [3] 98.05397 0.688556
#> [4] 5.14463 0.225563
#> -------
#> regions: 9 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
gi |> filter(gc > 0.1, score > 50)
#> GInteractions object with 2 interactions and 3 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | cis
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <Rle>
#> [1] chr1 1-10 * --- chr1 1-10 * | TRUE
#> [2] chr3 3-10 * --- chr3 1-10 * | TRUE
#> score gc
#> <numeric> <numeric>
#> [1] 73.532 0.530212
#> [2] 98.054 0.688556
#> -------
#> regions: 9 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
gi |> filter(cis)
#> GInteractions object with 4 interactions and 3 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | cis
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <Rle>
#> [1] chr1 1-10 * --- chr1 1-10 * | TRUE
#> [2] chr3 3-10 * --- chr3 1-10 * | TRUE
#> [3] chr4 4-10 * --- chr4 1-10 * | TRUE
#> [4] chr5 5-10 * --- chr5 1-10 * | TRUE
#> score gc
#> <numeric> <numeric>
#> [1] 73.53196 0.5302125
#> [2] 98.05397 0.6885560
#> [3] 74.15215 0.0312303
#> [4] 5.14463 0.2255625
#> -------
#> regions: 9 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
####################################################################
# 2. On-the-fly calculations
####################################################################
gi
#> GInteractions object with 5 interactions and 3 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | cis
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <Rle>
#> [1] chr1 1-10 * --- chr1 1-10 * | TRUE
#> [2] chr1 2-10 * --- chr2 1-10 * | FALSE
#> [3] chr3 3-10 * --- chr3 1-10 * | TRUE
#> [4] chr4 4-10 * --- chr4 1-10 * | TRUE
#> [5] chr5 5-10 * --- chr5 1-10 * | TRUE
#> score gc
#> <numeric> <numeric>
#> [1] 73.53196 0.5302125
#> [2] 19.59567 0.6958239
#> [3] 98.05397 0.6885560
#> [4] 74.15215 0.0312303
#> [5] 5.14463 0.2255625
#> -------
#> regions: 9 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
gi |> filter(start1 >= start2 + 3)
#> GInteractions object with 2 interactions and 3 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | cis
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <Rle>
#> [1] chr4 4-10 * --- chr4 1-10 * | TRUE
#> [2] chr5 5-10 * --- chr5 1-10 * | TRUE
#> score gc
#> <numeric> <numeric>
#> [1] 74.15215 0.0312303
#> [2] 5.14463 0.2255625
#> -------
#> regions: 9 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
gi |> filter(score * gc > score * 0.5)
#> GInteractions object with 3 interactions and 3 metadata columns:
#> seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | cis
#> <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <Rle>
#> [1] chr1 1-10 * --- chr1 1-10 * | TRUE
#> [2] chr1 2-10 * --- chr2 1-10 * | FALSE
#> [3] chr3 3-10 * --- chr3 1-10 * | TRUE
#> score gc
#> <numeric> <numeric>
#> [1] 73.5320 0.530212
#> [2] 19.5957 0.695824
#> [3] 98.0540 0.688556
#> -------
#> regions: 9 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths