pack: Range transformations of a `GenomicRanges` object for optimal file queries.

Description

Given a GRanges object, pack produces a GRangesList of the same ranges grouped and re-ordered.

Usage

"pack"(x, ..., range_len = 1e9, inter_range_len = 1e7)

Arguments

A GRanges object.

range_len

A numeric specifying the max length allowed for ranges in x.

inter_range_len

A numeric specifying the max length allowed between ranges in x.

...

Arguments passed to other methods.

Value

A GRanges object.

Details

Packing ranges The 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_len are packed in groups around the gap separating the distant ranges.

length: Ranges longer than range_len are packed `individually' (i.e., retrived from the file as a single range vs grouped with other ranges).

Utilities

: isPacked(x, ...): Returns a logical indicating if the ranges in x are packed. x must be a GRangesList object.

Examples

Run this code

## 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)