r-bioc-variantannotation 1.16.3-1 / usr / lib / R / site-library / VariantAnnotation / NAMESPACE

This file is indexed.

/usr/lib/R/site-library/VariantAnnotation/NAMESPACE is in r-bioc-variantannotation 1.16.3-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below. 

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
useDynLib(VariantAnnotation, .registration=TRUE)

import(methods)

import(BiocGenerics)

import(S4Vectors)

import(IRanges)

import(GenomeInfoDb)

import(GenomicRanges)

import(SummarizedExperiment)

import(Rsamtools)

importClassesFrom(Biobase, 
    AssayData
)

importFrom(Biobase,
    sampleNames, "sampleNames<-", samples
)

importClassesFrom(AnnotationDbi, 
    AnnotationDb
)

importMethodsFrom(AnnotationDbi, 
    colnames, exists, ncol, nrow,
    columns, keys, keytypes, select
)

importFrom(GenomicFeatures, 
    extractTranscriptSeqs, mapToTranscripts
)

importClassesFrom(GenomicFeatures, 
    TxDb
)

importMethodsFrom(GenomicFeatures, 
    cdsBy, exons, transcripts,
    fiveUTRsByTranscript, threeUTRsByTranscript,
    distance, mapToTranscripts
)

importFrom(XVector, "subseq", "subseq<-")

importFrom(Biostrings,
    AAStringSet, DNAStringSet, DNAStringSetList, DNA_BASES, getSeq
)

importMethodsFrom(Biostrings,
    nchar, reverseComplement, substr, translate
)

importClassesFrom(Biostrings, 
    DNAStringSet, DNAStringSetList
)

importMethodsFrom(DBI, 
    dbCommit, dbConnect, dbDisconnect, dbExistsTable, 
    dbGetQuery, dbReadTable, dbWriteTable, dbListTables, 
    dbListFields
)

importClassesFrom(BSgenome, 
    BSgenome
)

importMethodsFrom(BSgenome, 
    getSeq
)

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, genotypeCodesToNucleotides,
    tabulate, VRangesScanVcfParam, readVcfAsVRanges,
    isSNV, isInsertion, isDeletion, isIndel, isDelins, isTransition,
    isSubstitution,
    VcfFile, VcfFileList,
    makeVRangesFromGRanges
)

exportMethods(
    filterVcf, scanVcf, scanVcfHeader, ScanVcfParam,
    readVcf, writeVcf, expand,
    readVcfLongForm, ## Defunct
    predictCoding, getTranscriptSeqs, getSeq,
    genotypeToSnpMatrix, snpSummary,
    locateVariants, summarizeVariants,
    isSNV, isInsertion, isDeletion, isIndel, isDelins, isTransition,
    isSubstitution,

    fixed, "fixed<-", ref, "ref<-", alt, "alt<-", qual, "qual<-",
    filt, "filt<-", info, "info<-", geno, "geno<-", strand, 
    "strand<-", "[", "[<-", cbind, rbind, "mcols<-", 

    genome, seqlevels, seqinfo,

    reference, samples, header, meta,

    keys, keytypes, columns, select
)

APT Browse - Built by Thomas Orozco.