/usr/lib/R/site-library/GenomeInfoDb/NAMESPACE is in r-bioc-genomeinfodb 1.6.0-1.
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 | import(methods)
importFrom(stats4, summary)
import(BiocGenerics)
import(S4Vectors)
import(IRanges) # for CompressedList
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### Export non-generic functions
###
export(
## rankSeqlevels.R:
orderSeqlevels,
rankSeqlevels,
## fetchExtendedChromInfoFromUCSC.R:
fetchExtendedChromInfoFromUCSC,
## seqlevelsStyle.R:
genomeStyles,
extractSeqlevels,
extractSeqlevelsByGroup,
mapSeqlevels,
seqlevelsInGroup,
## seqlevels-wrappers.R:
keepSeqlevels, dropSeqlevels, renameSeqlevels, restoreSeqlevels,
keepStandardChromosomes,
## Seqinfo-class.R:
Seqinfo,
## GenomeDescription-classR:
GenomeDescription
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###
exportClasses(
Seqinfo,
GenomeDescription
)
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### 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
)
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### 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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