Range transformations of a GenomicRanges object for optimal file queries.
pack produces a
of the same ranges grouped and re-ordered.
A numeric specifying the max length allowed for ranges in
A numeric specifying the max length allowed between ranges in
Arguments passed to other methods.
pack method attempts to re-package ranges in optimal
form for extracting data from files. Ranges are not modified (made
shorter or longer) but re-ordered and / or re-grouped according
to the following criteria.
order: Ranges are ordered by genomic position within chromosomes.
distance: Ranges separted by a distance greater than the
inter_range_lenare packed in groups around the gap separating the distant ranges.
length: Ranges longer than
range_lenare packed ‘individually’ (i.e., retrived from the file as a single range vs grouped with other ranges).
isPacked(x, ...): Returns a logical indicating if the ranges in
xmust be a
unpackfor unpacking the result obtained with ‘packed’ ranges.
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## Ranges are ordered by position within chromosome. gr1 <- GRanges("chr1", IRanges(5:1*5, width = 3)) pack(gr1) ## Ranges separated by > inter_range_len are partitioned ## into groups defined by the endpoints of the gap. gr2 <- GRanges("chr2", IRanges(c(1:3, 30000:30003), width = 1000)) pack(gr2, inter_range_len = 20000) ## Ranges exceeding 'range_len' are isolated in a single element ## of the GRangesList. gr3 <- GRanges("chr3", IRanges(c(1:4), width=c(45, 1e8, 45, 45))) width(gr3) pack(gr3, range_len = 1e7)
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