Arrange a GInteractions by a column
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] 0.739944 0.7725215
#> [2] 46.639350 0.8746007
#> [3] 49.777739 0.1749406
#> [4] 28.976724 0.0342413
#> [5] 73.288199 0.3203857
#> -------
#> regions: 9 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
####################################################################
# 1. Arrange GInteractions by a numerical column
####################################################################
gi |> arrange(gc)
#> GInteractions object with 5 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] chr3 3-10 * --- chr3 1-10 * | TRUE
#> [3] chr5 5-10 * --- chr5 1-10 * | TRUE
#> [4] chr1 1-10 * --- chr1 1-10 * | TRUE
#> [5] chr1 2-10 * --- chr2 1-10 * | FALSE
#> score gc
#> <numeric> <numeric>
#> [1] 28.976724 0.0342413
#> [2] 49.777739 0.1749406
#> [3] 73.288199 0.3203857
#> [4] 0.739944 0.7725215
#> [5] 46.639350 0.8746007
#> -------
#> regions: 9 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
####################################################################
# 2. Arrange GInteractions by a logical column
####################################################################
gi |> arrange(cis)
#> 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 2-10 * --- chr2 1-10 * | FALSE
#> [2] chr1 1-10 * --- chr1 1-10 * | TRUE
#> [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] 46.639350 0.8746007
#> [2] 0.739944 0.7725215
#> [3] 49.777739 0.1749406
#> [4] 28.976724 0.0342413
#> [5] 73.288199 0.3203857
#> -------
#> regions: 9 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
####################################################################
# 3. Arrange GInteractions by a factor
####################################################################
gi |>
mutate(rep = factor(c("rep1", "rep2", "rep1", "rep2", "rep1"))) |>
arrange(rep)
#> GInteractions object with 5 interactions and 4 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] chr5 5-10 * --- chr5 1-10 * | TRUE
#> [4] chr1 2-10 * --- chr2 1-10 * | FALSE
#> [5] chr4 4-10 * --- chr4 1-10 * | TRUE
#> score gc rep
#> <numeric> <numeric> <factor>
#> [1] 0.739944 0.7725215 rep1
#> [2] 49.777739 0.1749406 rep1
#> [3] 73.288199 0.3203857 rep1
#> [4] 46.639350 0.8746007 rep2
#> [5] 28.976724 0.0342413 rep2
#> -------
#> regions: 9 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths
####################################################################
# 4. Combine sorting variables
####################################################################
gi |>
mutate(rep = factor(c("rep1", "rep2", "rep1", "rep2", "rep1"))) |>
arrange(dplyr::desc(rep), score)
#> GInteractions object with 5 interactions and 4 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] chr1 2-10 * --- chr2 1-10 * | FALSE
#> [3] chr1 1-10 * --- chr1 1-10 * | TRUE
#> [4] chr3 3-10 * --- chr3 1-10 * | TRUE
#> [5] chr5 5-10 * --- chr5 1-10 * | TRUE
#> score gc rep
#> <numeric> <numeric> <factor>
#> [1] 28.976724 0.0342413 rep2
#> [2] 46.639350 0.8746007 rep2
#> [3] 0.739944 0.7725215 rep1
#> [4] 49.777739 0.1749406 rep1
#> [5] 73.288199 0.3203857 rep1
#> -------
#> regions: 9 ranges and 0 metadata columns
#> seqinfo: 5 sequences from an unspecified genome; no seqlengths