unpack-methods: Un-pack results obtained with a pack()ed group of ranges

In Bioconductor/GenomicFiles: Distributed computing by file or by range

Un-pack results obtained with a pack()ed group of ranges

Description

unpack returns results obtained with pack()ed ranges to the geometry of the original, unpacked ranges.

Usage

## S4 method for signature 'list,GRangesList'
unpack(flesh, skeleton, ...)
## S4 method for signature 'List,GRangesList'
unpack(flesh, skeleton, ...)

Arguments

flesh	A List object to be unpacked; the result from querying a file with skeleton.
skeleton	The GRangesList created with 'pack(x)'.
...	Arguments passed to other methods.

Details

unpack returns a List obtained with packed ranges to the geometry and order of the original, unpacked ranges.

Value

A unpacked form of flesh.

See Also

• pack for packing ranges.

Examples

  fl <- system.file("extdata", "ex1.bam", package = "Rsamtools")
  gr <- GRanges(c(rep("seq2", 3), "seq1"), 
                IRanges(c(75, 1, 100, 1), width = 2))

  ## Ranges are packed by order within chromosome and grouped
  ## around gaps greater than 'inter_range_len'. See ?pack for details.
  pk <- pack(gr, inter_range_len = 25)

  ## FUN computes coverage for the range passed as 'rng'.
  FUN <- function(rng, fl, param) {
      requireNamespace("GenomicAlignments") ## for bamWhich() and coverage()
      Rsamtools::bamWhich(param) <- rng
      GenomicAlignments::coverage(Rsamtools::BamFile(fl), param=param)[rng]
  } 

  ## Compute coverage on the packed ranges.
  dat <- bplapply(as.list(pk), FUN, fl = fl, param = ScanBamParam())

  ## The result list contains RleLists of coverage.
  lapply(dat, class)

  ## unpack() transforms the results back to the order of 
  ## the original ranges (i.e., unpacked 'gr').
  unpack(dat, pk)

Bioconductor/GenomicFiles documentation built on Oct. 31, 2024, 7:01 a.m.