wigImport: WIG Import Functions. wigToGRanges (new) and wigToRangedData...

In gavinha/TitanCNA: Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Description

Fast fixedStep WIG file reading and parsing

Usage

wigToGRanges(wigfile, verbose = TRUE)
wigToRangedData(wigfile, verbose = TRUE)

Arguments

wigfile	Filepath to fixedStep WIG format file
verbose	Set to FALSE to suppress messages

Details

Reads the entire file into memory, then processes the file in rapid fashion, thus performance will be limited by memory capacity.

The WIG file is expected to conform to the minimal fixedStep WIG format (see References), where each chromsome is started by a “fixedStep” declaration line. The function assumes only a single track in the WIG file, and will ignore any lines before the first line starting with “fixedStep”.

Value

GRanges object with chromosome and position information, sorted in decreasing chromosal size and increasing position.

Author(s)

Gavin Ha, Daniel Lai

References

WIG

http://genome.ucsc.edu/goldenPath/help/wiggle.html

See Also

wigToGRanges is a wrapper around these functions for easy WIG file loading and structure formatting. It is modified from the HMMcopy package.

Examples

	map <- system.file("extdata", "map_chr2.wig", package = "TitanCNA")
	mScore <- as.data.frame(wigToGRanges(map))

gavinha/TitanCNA documentation built on April 22, 2021, 9:38 a.m.