VariantAnnotation-defunct

refLocsToLocalLocs

refLocsToLocalLocs,GRanges,TxDb,missing-method

refLocsToLocalLocs,GRanges,missing,GRangesList-method

readVcfLongForm

readVcfLongForm,TabixFile,character,GRanges-method

readVcfLongForm,TabixFile,character,missing-method

readVcfLongForm,TabixFile,character,RangesList-method

readVcfLongForm,TabixFile,character,ScanVcfParam-method

readVcfLongForm,character,character,ScanVcfParam-method

readVcfLongForm,character,character,missing-method

readVcfLongForm,character,missing,missing-method

dbSNPFilter

regionFilter

MatrixToSnpMatrix

VRangesScanVcfParam

restrictToSNV


  The functions or variables listed here are no longer part
  of <code>VariantAnnotation</code>.


Annotate variants, compute amino acid coding changes,
predict coding outcomes.

Bioconductor Package Maintainer

VariantAnnotation

Annotation of Genetic Variants

VariantAnnotation-defunct function

## Defunct in > 1.17.0
  <ul>
<li> VRangesScanVcfParam()
    </li>
<li> restrictToSNV()
  </li>
</ul> ## Removed
  <ul>
<li> refLocsToLocalLocs()
    </li>
<li> readVcfLongForm()
    </li>
<li> dbSNPFilter()
    </li>
<li> regionFilter()
    </li>
<li> MatrixToSnpMatrix()
    </li>
<li> getTranscriptSeqs()
  </li>
</ul> 

usage

Defunct Functions in Package <code>VariantAnnotation</code>

VariantAnnotation-defunct: Defunct Functions in Package `VariantAnnotation`

Description

Arguments

usage

Details

See Also