BigWigFile-class {rtracklayer}R Documentation

BigWigFile objects

Description

A BigWigFile object is a reference to a BigWig file. It exists to support methods with behavior particular to BigWig files.

Accessor Methods

In the code snippets below, x represents a BigWigFile object.

seqinfo(x): Gets the Seqinfo object indicating the lengths of the sequences for the intervals in the file. No circularity or genome information is available.

Import

import.bw(con, selection = BigWigSelection(ranges, ...), ranges = con, ...): Imports the intervals from a big wig file con, according to selection, a RangedSelection object indicating the intervals to retrieve from a bigWig file. Supported types of con include a BigWigFile and a file name. Note that this retrieval is very efficient, due to the indexing of the bigWig format.

Utilities

summary(ranges = as(seqinfo(object), "GenomicRanges"), size = 1L, type = c("mean", "min", "max", "coverage", "sd"), defaultValue = NA_real_): Aggregates the intervals in the file that fall into ranges, which should be something coercible to GRanges. The aggregation essentially compresses each sequence to a length of size. The algorithm is specified by type; available algorithms include the mean, min, max, coverage (percent sequence covered by at least one feature), and standard deviation. When a window contains no features, defaultValue is assumed. The result is an RleList, with an element for each element in ranges. The driving use case for this is visualization of coverage when the screen space is small compared to the viewed portion of the sequence. The operation is very fast, as it leverages cached multi-level summaries present in every BigWig file.

Author(s)

Michael Lawrence

See Also

import.bw and export.bw for reading and writing BigWig files, respectively.

Examples

bwf <- BigWigFile(system.file("tests", "test.bw", package = "rtracklayer"))
seqinfo(bwf)
track <- import.bw(bwf, asRangedData = FALSE)
summary(bwf) # for each sequence, average all values into one
summary(bwf, range(head(track))) # just average the first few features
summary(bwf, size = GenomicRanges::seqlengths(bwf) / 10) # 10X reduction
summary(bwf, type = "min") # min instead of mean

[Package rtracklayer version 1.14.1 Index]