exportGenotypeCallsAndConfidenceScores.BroadBirdseedGenotypeTcgaDataFile: Exports genotype calls and confidence scores

Description Arguments Details Author(s)

Description

Export genotype calls and corresponding confidence scores for one sample from a Birdseed data file to an AromaUnitGenotypeCallFile (genotype calls) and an AromaUnitSignalBinaryFile (confidence scores).

Arguments

dataSet

character, data set name.

unf

A UnitNamesFile.

...

arguments passed to AromaUnitGenotypeCallFile$allocateFromUnitNamesFile(...).

rootPath

character, root path for output files.

force

If TRUE, existing output files are rewritten.

verbose

Verbose object.

Details

A UnitNamesFile is inferred from "chipType" using AffymetrixCdfFile$byChipType(). Genotyping units (SNPs) are ordered according to this UnitNamesFile. Confidence scores are stored as one minus the input score as the latter is a p-value.

Author(s)

Pierre Neuvial.



Search within the aroma.tcga package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.