HMMcopy-output: WIG Output Functions

Description Usage Arguments Details Author(s) References See Also Examples

Description

Fast fixedStep WIG file formatting and output

Usage

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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

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


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