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

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

Usage

# S4 method for class 'list,GRangesList'
unpack(flesh, skeleton, ...)
# S4 method for class '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)
#> [[1]]
#> [1] "CompressedRleList"
#> attr(,"package")
#> [1] "IRanges"
#> 
#> [[2]]
#> [1] "CompressedRleList"
#> attr(,"package")
#> [1] "IRanges"
#> 
#> [[3]]
#> [1] "CompressedRleList"
#> attr(,"package")
#> [1] "IRanges"
#> 

  ## unpack() transforms the results back to the order of 
  ## the original ranges (i.e., unpacked 'gr').
  unpack(dat, pk)
#> RleList of length 4
#> $seq2
#> integer-Rle of length 2 with 2 runs
#>   Lengths:  1  1
#>   Values : 37 35
#> 
#> $seq2
#> integer-Rle of length 2 with 2 runs
#>   Lengths: 1 1
#>   Values : 3 4
#> 
#> $seq2
#> integer-Rle of length 2 with 2 runs
#>   Lengths:  1  1
#>   Values : 32 30
#> 
#> $seq1
#> integer-Rle of length 2 with 1 run
#>   Lengths: 2
#>   Values : 1
#>