pack-methods: Range transformations of a 'GenomicRanges' object for optimal...

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

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

## S4 method for signature 'GRanges'
pack(x, ..., range_len = 1e9, inter_range_len = 1e7)

Arguments

x	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.

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.

Value

A GRanges object.

See Also

• unpack for unpacking the result obtained with ‘packed’ ranges.

Examples

  ## 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)

Bioconductor/GenomicFiles documentation built on Oct. 27, 2023, 12:11 p.m.