Defunct Functions in Package ‘GWASTools’

Description

These functions are defunct and no longer available.

Details

The following functions are defunct; use the replacement indicated below:

• pedigreeClean: pedigreeCheck

• pedigreeFindDuplicates: pedigreeCheck

• ncdfCreate: createDataFile

• ncdfAddData: createDataFile

• ncdfAddIntensity: createAffyIntensityFile

• ncdfCheckGenotype: checkGenotypeFile

• ncdfCheckIntensity: checkIntensityFile

• ncdfSetMissingGenotypes: setMissingGenotypes

• gdsSetMissingGenotypes: setMissingGenotypes

• ncdfImputedDosage: imputedDosageFile

• gdsImputedDosage: imputedDosageFile

• gdsCheckImputedDosage: checkImputedDosageFile

• assocTestRegression: assocRegression

• assocTestCPH: assocCoxPH

• assocTestFisherExact: batchFisherTest

• gwasExactHW: exactHWE

• ncdfSubset: gdsSubset

• ncdfSubsetCheck: gdsSubsetCheck

• plinkToNcdf: snpgdsBED2GDS

• convertVcfGds: snpgdsVCF2GDS