HMMcopy-input: WIG Import Functions

In shahcompbio/HMMcopy: Copy number prediction with correction for GC and mappability bias for HTS data

Description

Fast fixedStep WIG file reading and parsing

Usage

wigToRangedData(wigfile, verbose = TRUE)
wigToArray(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

RangedData for wigToRangedData with chromosome and position information, sorted in decreasing chromosal size and increasing position.

Numeric array for wigToArray sorted in decreasing chromosal size and increasing position.

Author(s)

Daniel Lai

References

WIG

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

See Also

wigsToRangedData is a wrapper around these functions for easy WIG file loading and structure formatting.

Examples

  wigfile <- system.file("extdata", "tumour.wig", package = "HMMcopy")
  posAndValues <- wigToRangedData(wigfile)
  justValues <- wigToArray(wigfile)

shahcompbio/HMMcopy documentation built on Dec. 6, 2019, 12:47 a.m.