Defunct Functions in Package VariantAnnotation

The functions or variables listed here are no longer part of VariantAnnotation.

usage

## Removed

• refLocsToLocalLocs()

• readVcfLongForm()

• dbSNPFilter()

• regionFilter()

• MatrixToSnpMatrix()

• getTranscriptSeqs()

• VRangesScanVcfParam()

• restrictToSNV()

Details

## Removed

• refLocsToLocalLocs has been replaced by mapToTranscripts and pmapToTranscripts.

• readVcfLongForm has been replaced by expand.

• dbSNPFilter and regionFilter have been replaced by filterVcf.

• regionFilter has been replaced by filterVcf.

• MatrixToSnpMatrix has been replaced by genotypeToSnpMatrix.

• getTranscriptSeqs has been replaced by extractTranscriptSeqs in the GenomicFeatures package.

• VRangesScanVcfParam has been replaced by ScanVcfParam.

• restrictToSVN has been replaced by isSNV.

Author

Valerie Obenchain

See also

• expand

• filterVcf

• genotypeToSnpMatrix

• mapToTranscripts

• extractTranscriptSeqs

• isSNV

• ScanVcfParam