/usr/lib/R/site-library/GenomeInfoDb/NAMESPACE is in r-bioc-genomeinfodb 1.14.0-1.
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 | import(methods)
importFrom(utils, data, download.file, read.delim, read.table, read.csv)
importFrom(stats, setNames)
importFrom(stats4, summary)
importFrom(RCurl, getURL)
import(BiocGenerics)
import(S4Vectors)
import(IRanges) # for CompressedList
import(GenomeInfoDbData)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###
export(
## rankSeqlevels.R:
orderSeqlevels,
rankSeqlevels,
## fetchExtendedChromInfoFromUCSC.R:
fetchExtendedChromInfoFromUCSC,
## mapGenomeBuilds.R
mapGenomeBuilds,
genomeBuilds,
listOrganisms,
## seqlevelsStyle.R:
genomeStyles,
extractSeqlevels,
extractSeqlevelsByGroup,
mapSeqlevels,
seqlevelsInGroup,
## seqlevels-wrappers.R:
keepSeqlevels, dropSeqlevels, renameSeqlevels, restoreSeqlevels,
standardChromosomes, keepStandardChromosomes,
## Seqinfo-class.R:
Seqinfo,
## GenomeDescription-classR:
GenomeDescription
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###
exportClasses(
Seqinfo,
GenomeDescription
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S3 methods
###
S3method(summary, Seqinfo)
### 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(
summary.Seqinfo
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in GenomeInfoDb
###
exportMethods(
length,
names, "names<-",
"[",
as.data.frame,
show,
merge,
## Generics defined in the stats4 package:
summary,
## Generics defined in the BiocGenerics package:
intersect, organism, species
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics defined in GenomeInfoDb + export corresponding methods
###
export(
## seqinfo.R:
seqinfo, "seqinfo<-",
seqnames, "seqnames<-",
seqlevels, "seqlevels<-",
sortSeqlevels,
seqlevelsInUse,
seqlevels0,
seqlengths, "seqlengths<-",
isCircular, "isCircular<-",
genome, "genome<-",
## seqlevelsStyle.R:
seqlevelsStyle, "seqlevelsStyle<-",
## GenomeDescription-class.R:
commonName, provider, providerVersion,
releaseDate, releaseName, bsgenomeName,
available.species
)
exportMethods(
seqinfo,
seqnames, "seqnames<-",
seqlevels, "seqlevels<-",
sortSeqlevels,
seqlevelsInUse,
seqlengths, "seqlengths<-",
isCircular, "isCircular<-",
genome, "genome<-",
seqlevelsStyle, "seqlevelsStyle<-",
commonName, provider, providerVersion,
releaseDate, releaseName, bsgenomeName
)
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