HMMcopy-output: WIG Output Functions

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

Description

Fast fixedStep WIG file formatting and output

Usage

rangedDataToWig(correctOutput, file, column = "copy", sample = "R",
  verbose = TRUE)
rangedDataToSeg(correctOutput, file, column = "copy", sample = "R",
  verbose = TRUE)

Arguments

correctOutput	RangedData object for output, default options expect output from correctReadcount.
file	Filepath to write output to.
column	Column in input object to export. Defaults to corrected copy number.
sample	Sample name of the exported dataset, defaults to “R”
verbose	Set to FALSE to suppress messages.

Details

Assumes that all ranges in data set are non-overlapping windows of fixed width covering the entire genome. Note that positions in WIG files are 1-based while those in SEG files are 0-based.

Author(s)

Daniel Lai

References

WIG

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

SEG

http://www.broadinstitute.org/igv/SEG

See Also

correctReadcount output is the intended input

Examples

  data(tumour) # Load tumour_copy
  rangedDataToWig(tumour_copy, file = "test.wig")
  rangedDataToSeg(tumour_copy, file = "test.seg")

jujubix/HMMcopy documentation built on Nov. 27, 2021, 2:52 a.m.