mergeGRangesData {BRGenomics} | R Documentation

## Merge GRanges objects

### Description

Merges 2 or more GRanges objects by combining all of their ranges and associated signal (e.g. readcounts). If `multiplex = TRUE`, the input datasets are reversibly combined into a multiplexed GRanges containing a field for each input dataset.

### Usage

    mergeGRangesData(
      ...,
      field = "score",
      multiplex = FALSE,
      makeBRG = TRUE,
      exact_overlaps = FALSE,
      ncores = getOption("mc.cores", 2L)
    )

### Arguments

`...` | Any number of GRanges objects in which signal (e.g. readcounts) are contained within metadata. Lists of GRanges can also be passed, but they must be named lists if `multiplex = TRUE`. Multiple lists can be passed, but if any inputs are lists, then all inputs must be lists.
`field` | One or more input metadata fields to be combined, typically the "score" field. Fields typically contain coverage information. If only a single field is given (i.e. all input GRanges use the same field), that same field will be used for the output. Otherwise, the `"score"` metadata field will be used by default. The output metadata fields are different if `multiplex` is enabled.
`multiplex` | When set to `FALSE` (the default), input GRanges are merged irreversibly into a single new GRange, effectively combining the reads from different experiments. When `multiplex = TRUE`, the input GRanges data are reversibly combined into a multiplexed GRanges object, such that each input GRanges object has its own metadata field in the output.
`makeBRG` | If `TRUE` (the default), the output GRanges will be made "basepair-resolution" via `makeGRangesBRG`. This is always set to codeFALSE if `exact_overlaps = TRUE`.
`exact_overlaps` | By default (`FALSE`), any ranges that cover more than a single base are treated as "coverage" signal (see `getCountsByRegions`). If `exact_overlaps = TRUE`, all input ranges are conserved exactly as they are; ranges are only combined if they overlap exactly, and the signal of any combined range is the sum of the input ranges that were merged.
`ncores` | Number of cores to use for computations.

### Value

A disjoint, basepair-resolution (single-width) GRanges object comprised of all ranges found in the input GRanges objects.

If `multiplex = FALSE`, single fields from each input are combined into a single field in the output, the total signal of which is the sum of all input GRanges.

If `multiplex = TRUE`, each field of the output corresponds to an input GRanges object.

### Subsetting a multiplexed GRanges object

If `multiplex = TRUE`, the datasets are only combined into a single object, but the data themselves are not combined. To subset `field_i`, corresponding to input `dataset_i`:

`multi.gr <- mergeGRangesData(gr1, gr2, multiplex = TRUE)` `subset(multi.gr, gr1 != 0, select = gr1)` # select gr1

### Author(s)

Mike DeBerardine

### See Also

`makeGRangesBRG`

### Examples

    data("PROseq") # load included PROseq data

    #--------------------------------------------------#
    # divide & recombine PROseq (no overlapping positions)
    #--------------------------------------------------#

    thirds <- floor( (1:3)/3 * length(PROseq) )
    ps_1 <- PROseq[1:thirds[1]]
    ps_2 <- PROseq[(thirds[1]+1):thirds[2]]
    ps_3 <- PROseq[(thirds[2]+1):thirds[3]]

    # re-merge
    length(PROseq)
    length(ps_1)
    length(mergeGRangesData(ps_1, ps_2, ncores = 1))
    length(mergeGRangesData(ps_1, ps_2, ps_3, ncores = 1))

    #--------------------------------------------------#
    # combine PRO-seq with overlapping positions
    #--------------------------------------------------#

    gr1 <- PROseq[10:13]
    gr2 <- PROseq[12:15]

    PROseq[10:15]

    mergeGRangesData(gr1, gr2, ncores = 1)

    #--------------------------------------------------#
    # multiplex separate PRO-seq experiments
    #--------------------------------------------------#

    multi.gr <- mergeGRangesData(gr1, gr2, multiplex = TRUE, ncores = 1)
    multi.gr

    #--------------------------------------------------#
    # subset a multiplexed GRanges object
    #--------------------------------------------------#

    subset(multi.gr, gr1 > 0)

    subset(multi.gr, gr1 > 0, select = gr1)

[Package BRGenomics version 1.4.0 Index]