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useDynLib(VariantAnnotation, .registration=TRUE)
import(methods)
import(BiocGenerics)
import(Rsamtools)
import(GenomicRanges)
import(zlibbioc)
importClassesFrom(Biobase, AssayData)
importClassesFrom(AnnotationDbi, AnnotationDb)
importMethodsFrom(AnnotationDbi, colnames, cols, exists, keys, ncol,
nrow, select)
importFrom(GenomicFeatures, extractTranscriptsFromGenome)
importClassesFrom(GenomicFeatures, TranscriptDb)
importMethodsFrom(GenomicFeatures, cdsBy, exons, transcripts,
fiveUTRsByTranscript, threeUTRsByTranscript,
isActiveSeq, "isActiveSeq<-")
importFrom(IRanges, CharacterList, DataFrame, IRanges, isSingleString,
PartitioningByWidth, successiveViews, subsetByFilter, expand)
importClassesFrom(IRanges, DataFrame, Ranges, RangesList, RangedData)
importMethodsFrom(IRanges, "%in%", append, as.matrix, as.vector,
countOverlaps, elementLengths, end, eval, findOverlaps,
follow, gsub, lapply, match, "metadata<-", narrow, order,
precede, queryHits, rev, Rle, runValue, sapply, shift,
split, start, "start<-", subjectHits, "subseq<-", substring,
unlist, values, "values<-", which, width,
expand)
importMethodsFrom(DBI, dbCommit, dbConnect, dbDisconnect, dbExistsTable,
dbGetQuery, dbReadTable, dbWriteTable, dbListTables,
dbListFields)
importClassesFrom(BSgenome, BSgenome)
importFrom(utils, txtProgressBar, setTxtProgressBar)
#exportPattern("^[^\\.]")
exportClassPattern("^.*$")
export(VCF, VCFHeader,
vcfWhich, "vcfWhich<-", vcfFixed, "vcfFixed<-", vcfInfo, "vcfInfo<-",
vcfGeno, "vcfGeno<-", vcfTrimEmpty, "vcfTrimEmpty<-",
duplicateRSID, CodingVariants, IntronVariants,
FiveUTRVariants, ThreeUTRVariants, IntergenicVariants,
SpliceSiteVariants, PromoterVariants, AllVariants,
upstream, "upstream<-", downstream, "downstream<-",
probabilityToSnpMatrix, GLtoGP)
exportMethods(filterVcf,
scanVcf, scanVcfHeader, ScanVcfParam,
readVcf, readVcfLongForm, writeVcf,
predictCoding, getTranscriptSeqs, refLocsToLocalLocs,
MatrixToSnpMatrix, genotypeToSnpMatrix, snpSummary,
locateVariants, summarizeVariants,
fixed, "fixed<-", ref, "ref<-", alt, "alt<-", qual, "qual<-",
filt, "filt<-", info, "info<-", geno, "geno<-", strand,
"strand<-", "[", "[<-",
genome, seqlevels, renameSeqlevels, keepSeqlevels,
reference, samples, header, meta,
keys, cols, select)
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