distclu-functions {CAGEr} | R Documentation

## Private functions for distance clustering.

### Description

The flow of data is that a CTSS object of CTSSes is progressively deconstructed, and data to form the clusters is progressively integrated in a data.table object, which is finally converted to GRanges at the end. Doing the whole clustering with `GRanges` is more elegant, but looping on a `GRangesList` was just too slow. Maybe the operation on the `data.table` is more efficient because it is vectorised.

`.cluster.ctss.strand` does the strandless distance clustering of strandless CTSS positions from a single chromosome. Input does not need to be sorted, but pay attention that the output is sorted.

`.cluster.ctss.chr` does the stranded distance clustering of CTSS on a single chromosome, by dispatching both strands to `.cluster.ctss.strand` and merging the results, taking care keep the cluster IDs unique. Be careful that this function does not look at the score.

`.ctss2clusters` does the stranded distance clustering of CTSS.

`.summarize.clusters` calculates the number of CTSS, and the position and score of a main peak, for each cluster.

`.distclu` receives the data from the main `clusterCTSS` and dispatches each for (possibly parallel) processing.

### Usage

    .cluster.ctss.strand(ctss.ipos.chr, max.dist)

    .cluster.ctss.chr(ctss.chr, max.dist)

    .ctss2clusters(ctss, max.dist = 20, useMulticore = FALSE, nrCores = NULL)

    .summarize.clusters(ctss.clustered, removeSingletons = FALSE,
      keepSingletonsAbove = Inf)

    .distclu(se, max.dist = 20, removeSingletons = FALSE,
      keepSingletonsAbove = Inf, useMulticore = FALSE, nrCores = NULL)

### Arguments

`ctss.ipos.chr` | A IPos object.
`max.dist` | See `clusterCTSS()`.
`ctss.chr` | A CTSS.chr object.
`ctss` | A CTSS object with a score column.
`useMulticore, nrCores` | See clusterCTSS.
`ctss.clustered` | A `data.table` object representing the cluster ID (`id`), chromosome coordinates (`chr`, `pos`, `strand`) and the `score` of each CTSS.
`removeSingletons` | Remove “singleton” clusters that span only a single nucleotide ? (default = FALSE).
`keepSingletonsAbove` | Even if `removeSingletons = TRUE`, keep singletons when their score is aboove threshold (default = `Inf`).
`se` | A `SummarizedExperiment` object representing the CTSSes and their expression in each sample.

### Value

`.cluster.ctss.strand` returns an data.table object containing arbitrary cluster IDs (as integers) for each CTSS.

`.cluster.ctss.chr` returns a `data.table` object representing the chromosome coordinates (`chr`, `pos`, `strand`) of each CTSS, with their cluster ID (`id`).

`.ctss2clusters` returns a `data.table` object representing the cluster ID (`id`), chromosome coordinates (`chr`, `pos`, `strand`) and the `score` of each CTSS.

`.summarize.clusters` returns GRanges describing the clusters.

`.distclu` returns GRanges describing the clusters.

### Examples

    # Get example data
    library(IRanges)
    library(GenomicRanges)

    #.cluster.ctss.strand
    ctss.ipos.chr <- IPos(c(1,3,4,12,14,25,28))
    CAGEr:::.cluster.ctss.strand(ctss.ipos.chr, 5)

    ctss.chr <- CTSScoordinatesGR(exampleCAGEexp)
    ctss.chr <- ctss.chr[strand(ctss.chr) == "+"]
    ctss.ipos.chr <- ranges(ctss.chr)
    # Same result if not sorted
    identical(
      CAGEr:::.cluster.ctss.strand(ctss.ipos.chr, 20),
      CAGEr:::.cluster.ctss.strand(ctss.ipos.chr[sample(seq_along(ctss.ipos.chr))], 20)
    )
    # Returns an emtpy data.table object if given an empty IRanges object.
    identical(CAGEr:::.cluster.ctss.strand(IPos(), 20), data.table::data.table())

    #.cluster.ctss.chr
    ctss.chr <- CAGEr:::.CTSS.chr(CTSScoordinatesGR(exampleCAGEexp))
    CAGEr:::.cluster.ctss.chr(ctss.chr, 20)

    # .ctss2clusters
    ctss <- CAGEr:::.CTSS(CTSScoordinatesGR(exampleCAGEexp))
    score(ctss) <- CTSSnormalizedTpmDF(exampleCAGEexp)[[1]]
    seqnames(ctss)[rep(c(TRUE,FALSE), length(ctss) / 2)] <- "chr16"
    ctss
    clusters <- CAGEr:::.ctss2clusters(ctss, 20)
    clusters

    # .summarize.clusters
    CAGEr:::.summarize.clusters(clusters)
    CAGEr:::.summarize.clusters(clusters, removeSingletons = TRUE)
    CAGEr:::.summarize.clusters(clusters, removeSingletons = TRUE, keepSingletonsAbove = 5)

    # .distclu
    CAGEr:::.distclu(CTSStagCountSE(exampleCAGEexp))
    ## Not run:
    CAGEr:::.distclu(CTSStagCountSE(exampleCAGEexp), useMulticore = TRUE)

    ## End(Not run)

    CAGEr:::.distclu(CTSStagCountSE(exampleCAGEset))

[Package CAGEr version 1.22.3 Index]