mergeReplicates {BRGenomics} | R Documentation

## Merge replicates of basepair-resolution GRanges objects

### Description

This simple convenience function uses `mergeGRangesData` to combine replicates (e.g. biological replicates) of basepair-resolution GRanges objects.

### Usage

    mergeReplicates(
      ...,
      field = "score",
      sample_names = NULL,
      makeBRG = TRUE,
      exact_overlaps = FALSE,
      ncores = getOption("mc.cores", 2L)
    )

### Arguments

`...` | Either a list of GRanges objects, or any number of GRanges objects (see `mergeGRangesData`). However, the names of the datasets must end in `"_rep#"`, where "#" is one or more characters indicating the replicate.
`field` | The metadata field that contains count information for each range. `length(field)` should either be 1, or equal to the number of datasets.
`sample_names` | Optional character vector with which to rename the datasets. This is useful if the sample names do not conform to the "_rep" naming scheme.
`makeBRG, exact_overlaps` | See `mergeGRangesData`.
`ncores` | The number of cores to use. This function will try to maximize the use of the `ncores` given, but care should be taken as `mergeGRangesData` can be memory intensive. Excessive memory usage can cause dramatic reductions in performance.

### Value

A list of GRanges objects.

### Examples

    data("PROseq")
    ps_list <- list(a_rep1 = PROseq[seq(1, length(PROseq), 4)],
                    b_rep1 = PROseq[seq(2, length(PROseq), 4)],
                    a_rep2 = PROseq[seq(3, length(PROseq), 4)],
                    b_rep2 = PROseq[seq(4, length(PROseq), 4)])
    mergeReplicates(ps_list, ncores = 1)

[Package BRGenomics version 0.99.31 Index]