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VariantAnnotation (version 1.18.1)

VariantAnnotation-defunct: Defunct Functions in Package VariantAnnotation

Description

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

Usage

## Defunct in > 1.17.0
  
  • VRangesScanVcfParam()
  • restrictToSNV()
  ## Removed
  
  • refLocsToLocalLocs()
  • readVcfLongForm()
  • dbSNPFilter()
  • regionFilter()
  • MatrixToSnpMatrix()
  • getTranscriptSeqs()

Arguments

itemize

  • refLocsToLocalLocshas been replaced bymapToTranscriptsandpmapToTranscripts.

item

  • readVcfLongForm has been replaced by expand.
  • dbSNPFilter and regionFilter have been replaced by filterVcf.
  • regionFilter has been replaced by filterVcf.
  • MatrixToSnpMatrix has been replaced by genotypeToSnpMatrix.
  • getTranscriptSeqs has been replaced by extractTranscriptSeqs in the GenomicFeatures package.

Details

## Defunct in > 1.17.0
  • VRangesScanVcfParamhas been replaced byScanVcfParam.
restrictToSVN has been replaced by isSNV.

See Also