/usr/lib/R/site-library/BSgenome/NAMESPACE is in r-bioc-bsgenome 1.46.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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importFrom(utils, read.table, available.packages, contrib.url,
installed.packages, str)
importFrom(stats, setNames)
import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(GenomeInfoDb)
import(GenomicRanges)
import(XVector)
import(Biostrings)
import(Rsamtools)
import(rtracklayer)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###
exportClasses(
OnDiskLongTable_old,
GRanges_OR_NULL, OnDiskLongTable,
SNPlocs, ODLT_SNPlocs, OldFashionSNPlocs,
InjectSNPsHandler,
XtraSNPlocs,
BSgenome, MaskedBSgenome,
BSgenomeViews,
## BSgenomeForge classes:
BSgenomeDataPkgSeed
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S3 methods
###
S3method(as.data.frame, BSgenomeViews)
### We also export them thru the export() directive so that (a) they can be
### called directly, (b) tab-completion on the name of the generic shows them,
### and (c) methods() doesn't asterisk them.
export(
as.data.frame.BSgenomeViews
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in BSgenome
###
exportMethods(
## Methods for generics defined in the base package:
length, names,
dim, dimnames,
as.character, as.list, as.data.frame,
"[[", "$", unlist,
nchar,
## Methods for generics defined in the methods package:
coerce, show,
## Methods for generics defined in the BiocGenerics package:
start, end, width, strand, organism,
## Methods for generics defined in the S4Vectors package:
elementNROWS,
## Methods for generics defined in the IRanges package:
ranges, Views, subject, score,
## Methods for generics defined in the GenomeInfoDb package:
seqinfo, "seqinfo<-", seqnames, "seqnames<-",
commonName, provider, providerVersion, releaseDate, releaseName,
## Methods for generics defined in the GenomicRanges package:
granges,
## Methods for generics defined in the Biostrings package:
getSeq,
seqtype, alphabetFrequency, hasOnlyBaseLetters,
uniqueLetters, letterFrequency,
oligonucleotideFrequency, nucleotideFrequencyAt,
consensusMatrix, consensusString,
matchPWM, countPWM, vmatchPattern, vcountPattern,
## Methods for generics defined in the rtracklayer package:
export
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###
export(
## OnDiskLongTable_old-class.R:
saveAsOnDiskLongTable_old, saveRowidsForOnDiskLongTable_old,
OnDiskLongTable_old,
getBatchesFromOnDiskLongTable_old,
getRowsByIndexFromOnDiskLongTable_old, getRowsByIdFromOnDiskLongTable_old,
## OnDiskLongTable-class.R:
OnDiskLongTable, writeOnDiskLongTable, writeOnDiskLongTableRowids,
getBatchesFromOnDiskLongTable,
getBatchesBySeqnameFromOnDiskLongTable,
getBatchesByOverlapsFromOnDiskLongTable,
getRowsFromOnDiskLongTable,
getRowsByIdFromOnDiskLongTable,
## OldFashionSNPlocs-class.R:
newSNPlocs,
## XtraSNPlocs-class.R:
newXtraSNPlocs,
## BSgenome-class.R:
BSgenome, MaskedBSgenome,
## available.genomes.R:
installed.genomes, available.genomes, getBSgenome,
## injectSNPs.R:
installed.SNPs, available.SNPs,
## bsapply.R:
bsapply,
## BSgenomeViews-class.R:
BSgenomeViews,
## export-methods.R:
writeBSgenomeToFasta,
writeBSgenomeToTwobit,
## BSgenomeForge.R:
forgeSeqlengthsFile,
forgeSeqFiles,
forgeMasksFiles
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics defined in BSgenome + export corresponding methods
###
export(
## OnDiskLongTable_old-class.R:
breakpoints, blocksizes, rowids,
## OnDiskLongTable-class.R:
batchsizes, spatialIndex,
## SNPlocs-class.R:
referenceGenome, compatibleGenomes,
snpcount, snplocs,
snpsBySeqname, snpsByOverlaps, snpsById,
## OldFashionSNPlocs-class.R:
snpid2loc, snpid2alleles, snpid2grange,
## InjectSNPsHandler-class.R:
SNPlocs_pkgname,
## BSgenome-class.R:
sourceUrl,
mseqnames,
masknames,
## injectSNPs.R:
injectSNPs,
## BSgenomeForge.R:
forgeBSgenomeDataPkg,
forgeMaskedBSgenomeDataPkg
)
### Exactly the same list as above.
exportMethods(
breakpoints, blocksizes, rowids,
batchsizes, spatialIndex,
referenceGenome, compatibleGenomes,
snpcount, snplocs,
snpsBySeqname, snpsByOverlaps, snpsById,
snpid2loc, snpid2alleles, snpid2grange,
SNPlocs_pkgname,
sourceUrl,
mseqnames,
masknames,
injectSNPs,
forgeBSgenomeDataPkg,
forgeMaskedBSgenomeDataPkg
)
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