rtracklayer: BigWigSelection-class – R documentation

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BigWigSelection-class

Selection of ranges and columns

Description

A BigWigSelection represents a query against a BigWig file, see import.bw. It is simply a RangedSelection that requires its colnames parameter to be "score", if non-empty, as that is the only column supported by BigWig.

Constructor

: BigWigSelection(ranges = GRanges(), colnames = "score"): Constructs a BigWigSelection with the given ranges and colnames. ranges can be either something coercible to a IntegerRangesList, a character identifying a genome (see GenomicSelection), or a BigWigFile, in which case the ranges are derived from the bounds of its sequences.

Coercion

: as(from, "BigWigSelection"): Coerces from to a BigWigSelection object. Typically, from is a GRanges or a IntegerRangesList, the ranges of which become the ranges in the new BigWigSelection.

Author(s)

Michael Lawrence

Examples

rl <- IRangesList(chr1 = IRanges::IRanges(c(1, 5), c(3, 6)))

  BigWigSelection(rl)
  as(rl, "BigWigSelection") # same as above

  # do not select the 'score' column
  BigWigSelection(rl, character())

rtracklayer

R interface to genome annotation files and the UCSC genome browser

v1.50.0

Artistic-2.0 + file LICENSE

Authors

Michael Lawrence, Vince Carey, Robert Gentleman

Initial release