mergeGRangesData: Merge GRanges objects
In BRGenomics: Tools for the Efficient Analysis of High-Resolution Genomics Data

Description Usage Arguments Value Subsetting a multiplexed GRanges object Author(s) See Also Examples

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.

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

`...`	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.

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.

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

Mike DeBerardine

makeGRangesBRG

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)