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

View source: R/dataset_functions.R

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.

1 2 3 4 5 6 7 8 |

`...` |
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 |

`field` |
One or more |

`multiplex` |
When set to |

`makeBRG` |
If |

`exact_overlaps` |
By default ( |

`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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | ```
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)
``` |

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