/usr/lib/R/site-library/SummarizedExperiment/NAMESPACE is in r-bioc-summarizedexperiment 1.8.0-1.
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 | import(methods)
importFrom(utils, read.delim, .DollarNames)
importFrom(stats, setNames)
importFrom(tools, file_path_as_absolute)
importClassFrom(Matrix, Matrix) # for the "acbind" and "arbind" methods
import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(GenomeInfoDb)
import(GenomicRanges)
import(Biobase)
import(DelayedArray)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###
exportClasses(
Assays, ShallowData, ShallowSimpleListAssays,
SummarizedExperiment,
RangedSummarizedExperiment
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in SummarizedExperiment
###
exportMethods(
length, names, "names<-",
dim, dimnames, "dimnames<-",
"[", "[<-", "[[", "[[<-", "$", "$<-",
as.data.frame,
coerce,
show,
c,
merge,
Compare,
## Generics defined in BiocGenerics:
cbind, rbind,
duplicated, match,
is.unsorted, order, rank, sort,
start, "start<-", end, "end<-", width, "width<-",
strand, "strand<-",
updateObject,
## Generics defined in S4Vectors:
"metadata<-",
mcols, "mcols<-",
elementMetadata, "elementMetadata<-",
values, "values<-",
extractROWS, replaceROWS,
subset,
pcompare,
## Generics defined in IRanges:
ranges, "ranges<-",
shift, narrow, resize, flank, promoters, restrict, trim,
isDisjoint, disjointBins,
coverage,
findOverlaps,
precede, follow, nearest, distance, distanceToNearest,
## Generics defined in GenomeInfoDb:
seqinfo, "seqinfo<-",
seqnames, "seqnames<-",
## Generics defined in DelayedArray:
acbind, arbind,
rowRanges, realize
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###
export(
Assays,
.DollarNames.SummarizedExperiment,
.DollarNames.RangedSummarizedExperiment,
makeSummarizedExperimentFromExpressionSet,
makeSummarizedExperimentFromDataFrame,
naiveRangeMapper, probeRangeMapper, geneRangeMapper,
readKallisto, readKallistoBootstrap, KALLISTO_ASSAYS,
saveHDF5SummarizedExperiment, loadHDF5SummarizedExperiment
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics defined in SummarizedExperiment + export corresponding
### methods
###
export(
SummarizedExperiment,
"rowRanges<-",
rowData, "rowData<-",
colData, "colData<-",
assayNames, "assayNames<-",
assays, "assays<-",
assay, "assay<-"
)
### Exactly the same list as above.
exportMethods(
SummarizedExperiment,
"rowRanges<-",
rowData, "rowData<-",
colData, "colData<-",
assayNames, "assayNames<-",
assays, "assays<-",
assay, "assay<-"
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Register S3 methods
###
S3method(.DollarNames, SummarizedExperiment)
S3method(.DollarNames, RangedSummarizedExperiment)
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