MergedGInteractions Class

The `MergedGInteractions` class extends the `GInteractions` to contain additional information about the pairs being merged.

Value

A MergedGInteractions object (see description)

Details

The `MergedGInteractions` class uses a delegate object during initialization to assign its `GInteractions` slots. In addition to containing information from all pairs, it also behaves as a `GInteractions` object. `mergePairs()` builds this object.

Slots

delegate

A `GInteractions` object used to initialize `GInteractions`-specific slots. This is the mergedPairs set of interactions.

ids

An integer vector of ids linking indices in the `delegate` slot all pairs (`allPairs` slot). These indices are parallel to `delegate`.

allPairs

A `data.table` containing all input pairs combined. Also contains all metadata for each pair and 1) the source of the file, 2) an id, 3) which chromosome pair it belongs to (i.e. `grp`), and 4) the assigned cluster from `dbscan` (i.e. `clst`).

selectionMethod

Character describing which method was used to select the final pair from the cluster of merged pairs.

See also

[InteractionSet::GInteractions]

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
#> downloading 1 resources
#> retrieving 1 resource
#> 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")

class(x)
#> [1] "MergedGInteractions"
#> attr(,"package")
#> [1] "mariner"