defunct: Defunct Functions in Package 'VariantAnnotation'

In VariantAnnotation: Annotation of Genetic Variants

Description

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

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• refLocsToLocalLocs has been replaced by mapToTranscripts and pmapToTranscripts.

• readVcfLongForm has been replaced by expand.

• dbSNPFilter and regionFilter have been replaced by filterVcf.

• regionFilter has been replaced by filterVcf.

• MatrixToSnpMatrix has been replaced by genotypeToSnpMatrix.

• getTranscriptSeqs has been replaced by extractTranscriptSeqs in the GenomicFeatures package.

• VRangesScanVcfParam has been replaced by ScanVcfParam.

• restrictToSVN has been replaced by isSNV.

usage

## Removed

• refLocsToLocalLocs()

• readVcfLongForm()

• dbSNPFilter()

• regionFilter()

• MatrixToSnpMatrix()

• getTranscriptSeqs()

• VRangesScanVcfParam()

• restrictToSNV()

Author(s)

Valerie Obenchain

See Also

• expand

• filterVcf

• genotypeToSnpMatrix

• mapToTranscripts

• extractTranscriptSeqs

• isSNV

• ScanVcfParam

VariantAnnotation documentation built on Nov. 8, 2020, 5:08 p.m.