VariantAnnotation-defunct {VariantAnnotation} | R Documentation

## Defunct Functions in Package `VariantAnnotation`

### 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- `refLocsToLocalLocs` has been replaced by `mapToTranscripts` and `pmapToTranscripts`.

- `readVcfLongForm` has been replaced by `expand`.

- `dbSNPFilter` and `regionFilter` have been replaced by `filterVcf`.

- `regionFilter` has been replaced by `filterVcf`.

- `MatrixToSnpMatrix` has been replaced by `genotypeToSnpMatrix`.

- `getTranscriptSeqs` has been replaced by `extractTranscriptSeqs` in the GenomicFeatures package.

- `VRangesScanVcfParam` has been replaced by `ScanVcfParam`.

- `restrictToSVN` has been replaced by `isSNV`.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`

[Package VariantAnnotation version 1.30.1 Index]