unpack {GenomicFiles} | R Documentation |
unpack
returns results obtained with pack()ed ranges
to the geometry of the original, unpacked ranges.
## S4 method for signature 'list,GRangesList' unpack(flesh, skeleton, ...) ## S4 method for signature 'List,GRangesList' unpack(flesh, skeleton, ...)
flesh |
A |
skeleton |
The |
... |
Arguments passed to other methods. |
unpack
returns a List
obtained with
packed ranges to the geometry and order of the original,
unpacked ranges.
A unpacked form of flesh
.
pack
for packing ranges.
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)