Sets of paired range objects (i.e., `GInteractions`) are first clustered by genomic distance with `dbscan`, then a representative interaction is selected for each cluster.
Usage
mergePairs(
x,
radius,
method = "manhattan",
column = NULL,
selectMax = TRUE,
pos = "center"
)
# S4 method for list_OR_SimpleList_OR_GInteractions,numeric
mergePairs(
x,
radius,
method = "manhattan",
column = NULL,
selectMax = TRUE,
pos = "center"
)Arguments
- x
List of `GInteractions` or `data.frame`-like objects.
- radius
Numeric describing the distance in base pairs used to define a cluster or pairs.
- method
Character describing the distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". Any unambiguous substring can be given. Default is "manhattan".
- column
Character denoting the column to be used to select among clustered interactions.
- selectMax
Logical. TRUE (default) uses `which.max()` to select the interaction pair. FALSE uses `which.min()`. Only applicable when `column` is specified.
- pos
Positions used for clustering pairs. Must be one of "start", "end" or "center". Default is "center".
Details
Interactions are clustered into groups using the provided base pair `radius`, and distance `method` with `dbscan()`. Representative interactions are selected for each group by one of two methods. If `column` and `selectMax` arguments are provided, the representative interaction with the maximum (or minimum) value in `column` is returned for each cluster. If these parameters are missing, new ranges for each pair are returned by calculating the median of modes for each cluster.
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)
## Cluster & merge pairs
x <- mergePairs(x = giList,
radius = 10e03,
column = "APScoreAvg")
x
#> MergedGInteractions object with 1681 interactions and 9 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 110180000-110185000 --- chr9 111520000-111525000 |
#> [4] chr9 80375000-80380000 --- chr9 80650000-80655000 |
#> [5] chr9 108380000-108385000 --- chr9 108475000-108480000 |
#> ... ... ... ... ... ... .
#> [1677] chr7 27235000-27240000 --- chr7 27815000-27820000 |
#> [1678] chr7 86565000-86570000 --- chr7 86775000-86780000 |
#> [1679] chr7 95695000-95700000 --- chr7 96660000-96665000 |
#> [1680] chr7 116620000-116625000 --- chr7 116760000-116765000 |
#> [1681] chr7 140215000-140220000 --- chr7 140350000-140355000 |
#> color APScoreAvg ProbabilityofEnrichment RegAPScoreAvg
#> <character> <numeric> <numeric> <numeric>
#> [1] 0,0,0 2.61103 0.986044 1.41438
#> [2] 0,0,0 2.45301 0.982802 1.54370
#> [3] 0,0,0 3.40635 0.996545 1.80221
#> [4] 0,0,0 2.09352 0.946897 1.40194
#> [5] 0,0,0 2.14182 0.936547 1.41005
#> ... ... ... ... ...
#> [1677] 0,0,0 5.93708 0.999598 3.72133
#> [1678] 0,0,0 4.60998 0.993894 2.73905
#> [1679] 0,0,0 5.34541 0.999958 2.47288
#> [1680] 0,0,0 2.97086 0.969639 1.86991
#> [1681] 0,0,0 4.52114 0.993302 2.96563
#> Avg_diffMaxNeihgboor_1 Avg_diffMaxNeihgboor_2 avg std
#> <numeric> <numeric> <numeric> <numeric>
#> [1] 1.875585 2.12164 2.60512 0.794220
#> [2] 1.491568 1.60777 2.73756 0.856876
#> [3] 3.768934 3.89112 4.49898 1.492786
#> [4] 0.818514 1.10611 2.20826 0.589976
#> [5] 0.907892 1.01824 1.95072 0.543293
#> ... ... ... ... ...
#> [1677] 2.28945 3.41471 5.78381 1.175767
#> [1678] 2.07661 2.19518 3.25321 0.810704
#> [1679] 5.50065 5.70786 5.18389 2.052481
#> [1680] 1.32308 1.36217 2.31890 0.643926
#> [1681] 1.04456 2.16908 4.07791 0.663425
#> value
#> <numeric>
#> [1] 4.27231
#> [2] 4.06339
#> [3] 7.84915
#> [4] 2.93583
#> [5] 2.75773
#> ... ...
#> [1677] 7.81888
#> [1678] 5.09909
#> [1679] 10.07336
#> [1680] 3.49497
#> [1681] 5.00641
#> -------
#> regions: 2812 ranges and 0 metadata columns
#> seqinfo: 3 sequences from an unspecified genome; no seqlengths