Aggregate the metadata columns of merged pairs
Source:R/AllGenerics.R, R/methods-MergedGInteractions.R
aggMetadata.RdAggregate the metadata columns of merged pairs
Usage
aggMetadata(x, columns, funs)
# S4 method for MergedGInteractions,character,character_OR_function_OR_list
aggMetadata(x, columns, funs)Arguments
- x
MergedGInteractions object.
- columns
Character vector of columns to aggregate.
- funs
Character vector of functions to apply to `columns`.
Examples
## Load marinerData
if (!require("marinerData", quietly = TRUE))
BiocManager::install("marinerData")
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, read.table, header=TRUE, nrows=1000) |>
lapply(as_ginteractions) |>
setNames(gsub("^.*extdata/(.{2}).*$", "\\1", bedpeFiles))
## Add names describing the source and loop
giList <- lapply(seq_along(giList), \(i) {
x <- giList[[i]]
x$name <- paste0(names(giList)[i], "_loop_", length(x))
return(x)
})
## Cluster & merge pairs
x <- mergePairs(x = giList,
radius = 5e03)
## List loop names
aggMetadata(x, columns = "name", fun = "list")
#> MergedGInteractions object with 1786 interactions and 1 metadata column:
#> seqnames1 ranges1 seqnames2 ranges2 |
#> <Rle> <IRanges> <Rle> <IRanges> |
#> [1] chr9 118645000-118650000 --- chr9 119330000-119335000 |
#> [2] chr9 15280000-15285000 --- chr9 15405000-15410000 |
#> [3] chr9 17815000-17820000 --- chr9 18205000-18210000 |
#> [4] chr9 110180000-110185000 --- chr9 111520000-111525000 |
#> [5] chr9 80375000-80380000 --- chr9 80650000-80655000 |
#> ... ... ... ... ... ... .
#> [1782] chr7 33795000-33800000 --- chr7 33932500-33937500 |
#> [1783] chr7 25295000-25300000 --- chr7 25887500-25892500 |
#> [1784] chr7 86567500-86572500 --- chr7 86775000-86780000 |
#> [1785] chr7 116622500-116627500 --- chr7 116760000-116765000 |
#> [1786] chr7 140215000-140220000 --- chr7 140347500-140352500 |
#> list.name
#> <list>
#> [1] /home/runner/.cache/..
#> [2] /home/runner/.cache/..
#> [3] /home/runner/.cache/..
#> [4] /home/runner/.cache/..
#> [5] /home/runner/.cache/..
#> ... ...
#> [1782] /home/runner/.cache/..,/home/runner/.cache/..
#> [1783] /home/runner/.cache/..,/home/runner/.cache/..
#> [1784] /home/runner/.cache/..,/home/runner/.cache/..
#> [1785] /home/runner/.cache/..,/home/runner/.cache/..
#> [1786] /home/runner/.cache/..,/home/runner/.cache/..
#> -------
#> regions: 2962 ranges and 0 metadata columns
#> seqinfo: 3 sequences from an unspecified genome; no seqlengths
## Aggregate values
aggMetadata(x, columns = c("APScoreAvg"), fun = "mean")
#> MergedGInteractions object with 1786 interactions and 1 metadata column:
#> seqnames1 ranges1 seqnames2 ranges2 |
#> <Rle> <IRanges> <Rle> <IRanges> |
#> [1] chr9 118645000-118650000 --- chr9 119330000-119335000 |
#> [2] chr9 15280000-15285000 --- chr9 15405000-15410000 |
#> [3] chr9 17815000-17820000 --- chr9 18205000-18210000 |
#> [4] chr9 110180000-110185000 --- chr9 111520000-111525000 |
#> [5] chr9 80375000-80380000 --- chr9 80650000-80655000 |
#> ... ... ... ... ... ... .
#> [1782] chr7 33795000-33800000 --- chr7 33932500-33937500 |
#> [1783] chr7 25295000-25300000 --- chr7 25887500-25892500 |
#> [1784] chr7 86567500-86572500 --- chr7 86775000-86780000 |
#> [1785] chr7 116622500-116627500 --- chr7 116760000-116765000 |
#> [1786] chr7 140215000-140220000 --- chr7 140347500-140352500 |
#> mean.APScoreAvg
#> <numeric>
#> [1] 2.61103
#> [2] 2.45301
#> [3] 4.73751
#> [4] 3.40635
#> [5] 2.09352
#> ... ...
#> [1782] 2.89949
#> [1783] 5.40040
#> [1784] 4.60903
#> [1785] 2.86398
#> [1786] 4.48766
#> -------
#> regions: 2962 ranges and 0 metadata columns
#> seqinfo: 3 sequences from an unspecified genome; no seqlengths
aggMetadata(x, columns = c("APScoreAvg", "avg"), fun = "mean")
#> MergedGInteractions object with 1786 interactions and 2 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2 |
#> <Rle> <IRanges> <Rle> <IRanges> |
#> [1] chr9 118645000-118650000 --- chr9 119330000-119335000 |
#> [2] chr9 15280000-15285000 --- chr9 15405000-15410000 |
#> [3] chr9 17815000-17820000 --- chr9 18205000-18210000 |
#> [4] chr9 110180000-110185000 --- chr9 111520000-111525000 |
#> [5] chr9 80375000-80380000 --- chr9 80650000-80655000 |
#> ... ... ... ... ... ... .
#> [1782] chr7 33795000-33800000 --- chr7 33932500-33937500 |
#> [1783] chr7 25295000-25300000 --- chr7 25887500-25892500 |
#> [1784] chr7 86567500-86572500 --- chr7 86775000-86780000 |
#> [1785] chr7 116622500-116627500 --- chr7 116760000-116765000 |
#> [1786] chr7 140215000-140220000 --- chr7 140347500-140352500 |
#> mean.APScoreAvg mean.avg
#> <numeric> <numeric>
#> [1] 2.61103 2.60512
#> [2] 2.45301 2.73756
#> [3] 4.73751 4.68239
#> [4] 3.40635 4.49898
#> [5] 2.09352 2.20826
#> ... ... ...
#> [1782] 2.89949 2.08193
#> [1783] 5.40040 3.58636
#> [1784] 4.60903 3.34010
#> [1785] 2.86398 2.43657
#> [1786] 4.48766 3.98591
#> -------
#> regions: 2962 ranges and 0 metadata columns
#> seqinfo: 3 sequences from an unspecified genome; no seqlengths
aggMetadata(x, columns = c("APScoreAvg"), fun = c("mean", "median"))
#> MergedGInteractions object with 1786 interactions and 2 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2 |
#> <Rle> <IRanges> <Rle> <IRanges> |
#> [1] chr9 118645000-118650000 --- chr9 119330000-119335000 |
#> [2] chr9 15280000-15285000 --- chr9 15405000-15410000 |
#> [3] chr9 17815000-17820000 --- chr9 18205000-18210000 |
#> [4] chr9 110180000-110185000 --- chr9 111520000-111525000 |
#> [5] chr9 80375000-80380000 --- chr9 80650000-80655000 |
#> ... ... ... ... ... ... .
#> [1782] chr7 33795000-33800000 --- chr7 33932500-33937500 |
#> [1783] chr7 25295000-25300000 --- chr7 25887500-25892500 |
#> [1784] chr7 86567500-86572500 --- chr7 86775000-86780000 |
#> [1785] chr7 116622500-116627500 --- chr7 116760000-116765000 |
#> [1786] chr7 140215000-140220000 --- chr7 140347500-140352500 |
#> mean.APScoreAvg median.APScoreAvg
#> <numeric> <numeric>
#> [1] 2.61103 2.61103
#> [2] 2.45301 2.45301
#> [3] 4.73751 4.73751
#> [4] 3.40635 3.40635
#> [5] 2.09352 2.09352
#> ... ... ...
#> [1782] 2.89949 2.89949
#> [1783] 5.40040 5.40040
#> [1784] 4.60903 4.60903
#> [1785] 2.86398 2.86398
#> [1786] 4.48766 4.48766
#> -------
#> regions: 2962 ranges and 0 metadata columns
#> seqinfo: 3 sequences from an unspecified genome; no seqlengths
## Custom functions
aggMetadata(x, columns = c("APScoreAvg"), fun = \(x) {
ifelse(is.na(sd(x)), 0, sd(x))
})
#> MergedGInteractions object with 1786 interactions and 1 metadata column:
#> seqnames1 ranges1 seqnames2 ranges2 |
#> <Rle> <IRanges> <Rle> <IRanges> |
#> [1] chr9 118645000-118650000 --- chr9 119330000-119335000 |
#> [2] chr9 15280000-15285000 --- chr9 15405000-15410000 |
#> [3] chr9 17815000-17820000 --- chr9 18205000-18210000 |
#> [4] chr9 110180000-110185000 --- chr9 111520000-111525000 |
#> [5] chr9 80375000-80380000 --- chr9 80650000-80655000 |
#> ... ... ... ... ... ... .
#> [1782] chr7 33795000-33800000 --- chr7 33932500-33937500 |
#> [1783] chr7 25295000-25300000 --- chr7 25887500-25892500 |
#> [1784] chr7 86567500-86572500 --- chr7 86775000-86780000 |
#> [1785] chr7 116622500-116627500 --- chr7 116760000-116765000 |
#> [1786] chr7 140215000-140220000 --- chr7 140347500-140352500 |
#> fun1.APScoreAvg
#> <numeric>
#> [1] 0
#> [2] 0
#> [3] 0
#> [4] 0
#> [5] 0
#> ... ...
#> [1782] 0.03410843
#> [1783] 0.96721962
#> [1784] 0.00133997
#> [1785] 0.15114917
#> [1786] 0.04735593
#> -------
#> regions: 2962 ranges and 0 metadata columns
#> seqinfo: 3 sequences from an unspecified genome; no seqlengths