Merge replicates of basepair-resolution GRanges objects

Source: R/dataset_functions.R

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

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)
#> $a
#> GRanges object with 23690 ranges and 1 metadata column:
#>           seqnames    ranges strand |     score
#>              <Rle> <IRanges>  <Rle> | <integer>
#>       [1]     chr4      1295      + |         1
#>       [2]     chr4     42588      + |         1
#>       [3]     chr4     42593      + |         5
#>       [4]     chr4     42595      + |         1
#>       [5]     chr4     42601      + |         1
#>       ...      ...       ...    ... .       ...
#>   [23686]     chr4   1307122      - |         1
#>   [23687]     chr4   1307283      - |         1
#>   [23688]     chr4   1307301      - |         1
#>   [23689]     chr4   1316537      - |         1
#>   [23690]     chr4   1319004      - |         1
#>   -------
#>   seqinfo: 7 sequences from an unspecified genome
#> 
#> $b
#> GRanges object with 23690 ranges and 1 metadata column:
#>           seqnames    ranges strand |     score
#>              <Rle> <IRanges>  <Rle> | <integer>
#>       [1]     chr4     41428      + |         1
#>       [2]     chr4     42590      + |         2
#>       [3]     chr4     42594      + |         2
#>       [4]     chr4     42596      + |         1
#>       [5]     chr4     42618      + |         1
#>       ...      ...       ...    ... .       ...
#>   [23686]     chr4   1307126      - |         1
#>   [23687]     chr4   1307300      - |         1
#>   [23688]     chr4   1307742      - |         1
#>   [23689]     chr4   1318960      - |         1
#>   [23690]     chr4   1319369      - |         1
#>   -------
#>   seqinfo: 7 sequences from an unspecified genome
#>