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useDynLib(VariantAnnotation, .registration=TRUE)
import(methods)
import(BiocGenerics)
import(Rsamtools)
import(GenomicRanges)
importClassesFrom(Biobase,
AssayData
)
importFrom(Biobase,
sampleNames, "sampleNames<-", samples
)
importClassesFrom(AnnotationDbi,
AnnotationDb
)
importMethodsFrom(AnnotationDbi,
colnames, exists, ncol, nrow,
columns, keys, keytypes, select
)
importFrom(GenomicFeatures,
extractTranscriptSeqs
)
importClassesFrom(GenomicFeatures,
TranscriptDb
)
importMethodsFrom(GenomicFeatures,
cdsBy, exons, transcripts,
fiveUTRsByTranscript, threeUTRsByTranscript,
isActiveSeq, "isActiveSeq<-",
distance
)
importFrom(IRanges,
CharacterList, DataFrame, DataFrameList, FilterRules, IntegerList,
IRanges, isSingleNumber, isSingleString, isTRUEorFALSE, LogicalList,
NumericList, PartitioningByEnd, PartitioningByWidth, seqsplit,
SimpleList, splitAsList, successiveViews, FilterMatrix, expand,
isSingleNumberOrNA, endoapply, metadata, filterRules, subsetByFilter
)
importClassesFrom(IRanges,
CharacterList, DataFrame, Ranges, RangesList, RangedData,
SimpleDataFrameList, SimpleList, FilterRules, FilterMatrix
)
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, substring,
unlist, values, "values<-", which, width,
expand, ifelse, as.factor, relist, subsetByFilter, selfmatch, unstrsplit
)
importFrom(XVector, "subseq", "subseq<-")
importFrom(Biostrings,
AAStringSet, DNAStringSet, DNAStringSetList, DNA_BASES
)
importMethodsFrom(Biostrings,
nchar, reverseComplement, substr, translate
)
importClassesFrom(Biostrings,
DNAStringSet, DNAStringSetList
)
importMethodsFrom(DBI,
dbCommit, dbConnect, dbDisconnect, dbExistsTable,
dbGetQuery, dbReadTable, dbWriteTable, dbListTables,
dbListFields
)
importClassesFrom(BSgenome,
BSgenome
)
importFrom(rtracklayer,
liftOver
)
importFrom(utils,
txtProgressBar, setTxtProgressBar
)
exportClassPattern("^.*$")
export(
VCF, VCFHeader, reference,
header, "header<-", meta, "meta<-",
vcfWhich, "vcfWhich<-", vcfFixed, "vcfFixed<-", vcfInfo, "vcfInfo<-",
vcfGeno, "vcfGeno<-", vcfSamples, "vcfSamples<-", vcfTrimEmpty,
"vcfTrimEmpty<-",
duplicateRSID, CodingVariants, IntronVariants,
FiveUTRVariants, ThreeUTRVariants, IntergenicVariants,
SpliceSiteVariants, PromoterVariants, AllVariants,
upstream, "upstream<-", downstream, "downstream<-",
promoter, "promoter<-", intergenic, "intergenic<-",
probabilityToSnpMatrix, GLtoGP, restrictToSNV,
VRanges, VRangesList, asVCF, softFilter, resetFilter,
totalDepth, altDepth, refDepth, sampleNames, "sampleNames<-", altFraction,
softFilterMatrix, "softFilterMatrix<-", hardFilters, "hardFilters<-",
called, stackSamples, "altDepth<-", "refDepth<-", "totalDepth<-",
probabilityToSnpMatrix, GLtoGP,
readInfo, readGeno, readGT,
tabulate, VRangesScanVcfParam, readVcfAsVRanges,
isSNV, isInsertion, isDeletion, isIndel, isTransition,
isSubstitution
)
exportMethods(
filterVcf, scanVcf, scanVcfHeader, ScanVcfParam,
readVcf, writeVcf, expand,
readVcfLongForm, ## Defunct
predictCoding, getTranscriptSeqs, refLocsToLocalLocs,
genotypeToSnpMatrix, snpSummary,
locateVariants, summarizeVariants,
isSNV, isInsertion, isDeletion, isIndel, isTransition,
isSubstitution,
fixed, "fixed<-", ref, "ref<-", alt, "alt<-", qual, "qual<-",
filt, "filt<-", info, "info<-", geno, "geno<-", strand,
"strand<-", "[", "[<-", cbind, rbind, "mcols<-",
genome, seqlevels,
reference, samples, header, meta,
keys, keytypes, columns, select
)
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