exportGenotypeCallsAndConfidenceScores.BroadBirdseedGenotypeTcgaDataFile: Exports genotype calls and confidence scores

In HenrikBengtsson/aroma.tcga: Methods for accessing online The Cancer Genome Atlas (TCGA) data

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.

HenrikBengtsson/aroma.tcga documentation built on May 7, 2019, 2:51 a.m.