VariantAnnotation
VariantAnnotation
.
VRangesScanVcfParam
has been replaced by ScanVcfParam
.
restrictToSVN
has been replaced by isSNV
.
## 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has been replaced by mapToTranscripts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has been replaced by expand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have been replaced by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has been replaced by filterVcf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has been replaced by genotypeToSnpMatrix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has been replaced by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.