Get clustered pairs from MergedGInteractions object
Source:R/AllGenerics.R, R/methods-MergedGInteractions.R
clusters.RdReturns the clustered pairs associated with each range in the `MergedGInteractions` object. Order always follows the indices of the `MergedGInteractions` object.
Examples
## Load required packages
library(data.table, include.only="fread")
## Load marinerData
if (!require("marinerData", quietly = TRUE))
BiocManager::install("marinerData")
## Reference BEDPE files (loops called with SIP)
bedpeFiles <- c(
marinerData::FS_5kbLoops.txt(),
marinerData::WT_5kbLoops.txt()
)
#> see ?marinerData and browseVignettes('marinerData') for documentation
#> loading from cache
#> see ?marinerData and browseVignettes('marinerData') for documentation
#> loading from cache
names(bedpeFiles) <- c("FS", "WT")
## Read in bedpeFiles as a list of GInteractions
## Use only first 1000 rows for fast example
giList <-
lapply(bedpeFiles, fread, nrows = 1000) |>
lapply(as_ginteractions)
## Cluster & merge pairs
x <- mergePairs(x = giList,
radius = 10e03,
column = "APScoreAvg")
## Access pair clusters
clusters(x[1:3])
#> [[1]]
#> seqnames1 start1 end1 width1 strand1 seqnames2 start2 end2
#> <fctr> <int> <int> <int> <fctr> <fctr> <int> <int>
#> 1: chr9 118645000 118650000 5001 * chr9 119330000 119335000
#> width2 strand2 color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg
#> <int> <fctr> <char> <num> <num> <num>
#> 1: 5001 * 0,0,0 2.611034 0.9860443 1.414376
#> Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2 avg std value
#> <num> <num> <num> <num> <num>
#> 1: 1.875585 2.121637 2.605124 0.7942202 4.272311
#> src
#> <char>
#> 1: FS
#>
#> [[2]]
#> seqnames1 start1 end1 width1 strand1 seqnames2 start2 end2
#> <fctr> <int> <int> <int> <fctr> <fctr> <int> <int>
#> 1: chr9 15280000 15285000 5001 * chr9 15405000 15410000
#> width2 strand2 color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg
#> <int> <fctr> <char> <num> <num> <num>
#> 1: 5001 * 0,0,0 2.453013 0.9828022 1.543698
#> Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2 avg std value
#> <num> <num> <num> <num> <num>
#> 1: 1.491568 1.607766 2.737556 0.856876 4.063394
#> src
#> <char>
#> 1: FS
#>
#> [[3]]
#> seqnames1 start1 end1 width1 strand1 seqnames2 start2 end2
#> <fctr> <int> <int> <int> <fctr> <fctr> <int> <int>
#> 1: chr9 110180000 110185000 5001 * chr9 111520000 111525000
#> width2 strand2 color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg
#> <int> <fctr> <char> <num> <num> <num>
#> 1: 5001 * 0,0,0 3.406346 0.9965453 1.802207
#> Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2 avg std value
#> <num> <num> <num> <num> <num>
#> 1: 3.768934 3.891115 4.498982 1.492786 7.849146
#> src
#> <char>
#> 1: FS
#>
clusters(x[3:1])
#> [[1]]
#> seqnames1 start1 end1 width1 strand1 seqnames2 start2 end2
#> <fctr> <int> <int> <int> <fctr> <fctr> <int> <int>
#> 1: chr9 110180000 110185000 5001 * chr9 111520000 111525000
#> width2 strand2 color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg
#> <int> <fctr> <char> <num> <num> <num>
#> 1: 5001 * 0,0,0 3.406346 0.9965453 1.802207
#> Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2 avg std value
#> <num> <num> <num> <num> <num>
#> 1: 3.768934 3.891115 4.498982 1.492786 7.849146
#> src
#> <char>
#> 1: FS
#>
#> [[2]]
#> seqnames1 start1 end1 width1 strand1 seqnames2 start2 end2
#> <fctr> <int> <int> <int> <fctr> <fctr> <int> <int>
#> 1: chr9 15280000 15285000 5001 * chr9 15405000 15410000
#> width2 strand2 color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg
#> <int> <fctr> <char> <num> <num> <num>
#> 1: 5001 * 0,0,0 2.453013 0.9828022 1.543698
#> Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2 avg std value
#> <num> <num> <num> <num> <num>
#> 1: 1.491568 1.607766 2.737556 0.856876 4.063394
#> src
#> <char>
#> 1: FS
#>
#> [[3]]
#> seqnames1 start1 end1 width1 strand1 seqnames2 start2 end2
#> <fctr> <int> <int> <int> <fctr> <fctr> <int> <int>
#> 1: chr9 118645000 118650000 5001 * chr9 119330000 119335000
#> width2 strand2 color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg
#> <int> <fctr> <char> <num> <num> <num>
#> 1: 5001 * 0,0,0 2.611034 0.9860443 1.414376
#> Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2 avg std value
#> <num> <num> <num> <num> <num>
#> 1: 1.875585 2.121637 2.605124 0.7942202 4.272311
#> src
#> <char>
#> 1: FS
#>
clusters(x[c(3, 1, 2)])
#> [[1]]
#> seqnames1 start1 end1 width1 strand1 seqnames2 start2 end2
#> <fctr> <int> <int> <int> <fctr> <fctr> <int> <int>
#> 1: chr9 110180000 110185000 5001 * chr9 111520000 111525000
#> width2 strand2 color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg
#> <int> <fctr> <char> <num> <num> <num>
#> 1: 5001 * 0,0,0 3.406346 0.9965453 1.802207
#> Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2 avg std value
#> <num> <num> <num> <num> <num>
#> 1: 3.768934 3.891115 4.498982 1.492786 7.849146
#> src
#> <char>
#> 1: FS
#>
#> [[2]]
#> seqnames1 start1 end1 width1 strand1 seqnames2 start2 end2
#> <fctr> <int> <int> <int> <fctr> <fctr> <int> <int>
#> 1: chr9 118645000 118650000 5001 * chr9 119330000 119335000
#> width2 strand2 color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg
#> <int> <fctr> <char> <num> <num> <num>
#> 1: 5001 * 0,0,0 2.611034 0.9860443 1.414376
#> Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2 avg std value
#> <num> <num> <num> <num> <num>
#> 1: 1.875585 2.121637 2.605124 0.7942202 4.272311
#> src
#> <char>
#> 1: FS
#>
#> [[3]]
#> seqnames1 start1 end1 width1 strand1 seqnames2 start2 end2
#> <fctr> <int> <int> <int> <fctr> <fctr> <int> <int>
#> 1: chr9 15280000 15285000 5001 * chr9 15405000 15410000
#> width2 strand2 color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg
#> <int> <fctr> <char> <num> <num> <num>
#> 1: 5001 * 0,0,0 2.453013 0.9828022 1.543698
#> Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2 avg std value
#> <num> <num> <num> <num> <num>
#> 1: 1.491568 1.607766 2.737556 0.856876 4.063394
#> src
#> <char>
#> 1: FS
#>
clusters(x) |> length()
#> [1] 1681