GenomicFeatures/NAMESPACE at devel · Bioconductor/GenomicFeatures · GitHub

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useDynLib(GenomicFeatures)

import(methods)
importFrom(stats, setNames)
importFrom(utils, as.person)

importMethodsFrom(DBI, dbGetQuery, dbListTables, dbListFields)

import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(Seqinfo)
import(XVector)
import(GenomicRanges)
import(AnnotationDbi)

importClassesFrom(Biostrings, DNAString, DNAStringSet, MaskedDNAString)
importFrom(Biostrings, DNAStringSet, reverseComplement, getSeq)

importFrom(rtracklayer, asBED, asGFF)


exportClasses(TxDb, FeatureDb)

export(
  ## id2name.R:
  id2name,

  ## transcripts.R:
  transcripts, exons, cds, genes,

  ## transcriptsBy.R:
  transcriptsBy,
  exonsBy,
  cdsBy,
  intronsByTranscript,
  fiveUTRsByTranscript,
  threeUTRsByTranscript,

  ## transcriptsByOverlaps.R:
  transcriptsByOverlaps,
  exonsByOverlaps,
  cdsByOverlaps,

  ## transcriptLengths.R:
  transcriptLengths,

  ## exonicParts.R:
  tidyTranscripts, tidyExons, tidyIntrons,
  exonicParts, intronicParts,

  ## extendExonsIntoIntrons.R:
  extendExonsIntoIntrons,

  ## features.R:
  features,

  ## tRNAs.R:
  tRNAs,

  ## extractTranscriptSeqs.R:
  extractTranscriptSeqs,

  ## extractUpstreamSeqs.R:
  extractUpstreamSeqs,

  ## getPromoterSeq-methods.R:
  getPromoterSeq, getTerminatorSeq,

  ## transcriptLocs2refLocs.R:
  transcriptLocs2refLocs,
  transcriptWidths,

  ## coordinate-mapping-methods.R:
  mapToTranscripts, pmapToTranscripts,
  mapFromTranscripts, pmapFromTranscripts,

  ## proteinToGenome.R:
  proteinToGenome,

  ## coverageByTranscript.R:
  coverageByTranscript,
  pcoverageByTranscript
)

exportMethods(
  organism,
  show,
  as.list,
  seqlevels0, "seqlevels<-", seqinfo,
  transcripts, exons, cds, genes,
  promoters, terminators,
  transcriptsByOverlaps,
  exonsByOverlaps,
  cdsByOverlaps,
  transcriptsBy,
  exonsBy,
  cdsBy,
  intronsByTranscript,
  fiveUTRsByTranscript,
  threeUTRsByTranscript,
  tRNAs,
  extractTranscriptSeqs,
  extractUpstreamSeqs,
  getPromoterSeq, getTerminatorSeq,
  isActiveSeq,
  "isActiveSeq<-",
  asBED, asGFF,
  distance,
  mapToTranscripts, pmapToTranscripts,
  mapFromTranscripts, pmapFromTranscripts,
  mapIdsToRanges, mapRangesToIds,
  proteinToGenome
)