Bioconductor/SummarizedExperiment
A container (S4 class) for matrix-like assays

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Search the Bioconductor/SummarizedExperiment package
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Functions
267
Source code
28
Man pages
11
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Bioconductor/SummarizedExperiment: A container (S4 class) for matrix-like assays
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API

API for Bioconductor/SummarizedExperiment
A container (S4 class) for matrix-like assays

Global functions
$,SummarizedExperiment-method Man page
$<-,SummarizedExperiment-method Man page
.DollarNames.SummarizedExperiment Source code
.RangedSummarizedExperiment.Compare Source code
.RangedSummarizedExperiment.pcompare Source code
.SummarizedExperiment.assays.replace Source code
.SummarizedExperiment.charbound Source code
.SummarizedExperiment.rowRanges.replace Source code
.assays_have_expected_dimnames Source code
.bind_Assays_objects Source code
.bind_assays Source code
.cbind.DataFrame Source code
.cbind.SummarizedExperiment Source code
.compare Source code
.extract_Assays_subset Source code
.from_AnnotatedDataFrame_to_DataFrame Source code
.from_DataFrame_to_AnnotatedDataFrame Source code
.from_GRangesList_to_FeatureData Source code
.from_GRanges_to_FeatureData Source code
.from_RangedSummarizedExperiment_to_SummarizedExperiment Source code
.from_SummarizedExperiment_to_RangedSummarizedExperiment Source code
.from_rowRanges_to_FeatureData Source code
.get_colnames_from_first_assay Source code
.get_rownames_from_first_assay Source code
.loom_make_rownames Source code
.rbind.SummarizedExperiment Source code
.replace_Assays_subset Source code
.set_RangedSummarizedExperiment_seqinfo Source code
.test Source code
.updateObject_Assays Source code
.updateObject_RangedSummarizedExperiment Source code
.updateObject_SummarizedExperiment Source code
.valid.Assays Source code
.valid.RangedSummarizedExperiment Source code
.valid.SummarizedExperiment Source code
.valid.SummarizedExperiment.assays_dim Source code
.valid.SummarizedExperiment.assays_ncol Source code
.valid.SummarizedExperiment.assays_nrow Source code
Assays Man page Source code
Assays-class Man page
AssaysInEnv Man page
AssaysInEnv-class Man page
Assays_OR_NULL Man page
Assays_OR_NULL-class Man page
Compare,ANY,RangedSummarizedExperiment-method Man page
Compare,RangedSummarizedExperiment,ANY-method Man page
Compare,RangedSummarizedExperiment,RangedSummarizedExperiment-me Man page
RangedSummarizedExperiment Man page
RangedSummarizedExperiment-class Man page
ShallowData Man page
ShallowData-class Man page
ShallowSimpleListAssays Man page
ShallowSimpleListAssays-class Man page
SimpleAssays Man page
SimpleAssays-class Man page
SummarizedExperiment Man page Source code
SummarizedExperiment-class Man page
[,Assays,ANY,ANY,ANY-method Man page
[,Assays,ANY-method Man page
[,SummarizedExperiment,ANY,ANY,ANY-method Man page
[,SummarizedExperiment,ANY-method Man page
[,SummarizedExperiment-method Man page
[<-,Assays,ANY,ANY,ANY-method Man page
[<-,SummarizedExperiment,ANY,ANY,SummarizedExperiment-method Man page
[[,SummarizedExperiment,ANY,missing-method Man page
[[<-,SummarizedExperiment,ANY,missing-method Man page
acbind,Matrix-method Man page
arbind,Matrix-method Man page
assay Man page
assay,SummarizedExperiment,character-method Man page
assay,SummarizedExperiment,missing-method Man page
assay,SummarizedExperiment,numeric-method Man page
assay<- Man page
assay<-,SummarizedExperiment,character-method Man page
assay<-,SummarizedExperiment,missing-method Man page
assay<-,SummarizedExperiment,numeric-method Man page
assayNames Man page
assayNames,SummarizedExperiment-method Man page
assayNames<- Man page
assayNames<-,SummarizedExperiment,character-method Man page
assays Man page
assays,SummarizedExperiment-method Man page
assays<- Man page
assays<-,SummarizedExperiment,SimpleList-method Man page
assays<-,SummarizedExperiment,list-method Man page
cbind,Assays-method Man page
cbind,SummarizedExperiment-method Man page
class:Assays Man page
class:AssaysInEnv Man page
class:Assays_OR_NULL Man page
class:RangedSummarizedExperiment Man page
class:ShallowData Man page
class:ShallowSimpleListAssays Man page
class:SimpleAssays Man page
class:SummarizedExperiment Man page
coerce,AssaysInEnv,SimpleList-method Man page
coerce,ExpressionSet,RangedSummarizedExperiment-method Man page
coerce,ExpressionSet,SummarizedExperiment-method Man page
coerce,RangedSummarizedExperiment,ExpressionSet-method Man page
coerce,RangedSummarizedExperiment,SummarizedExperiment-method Man page
coerce,ShallowSimpleListAssays,SimpleList-method Man page
coerce,SimpleAssays,SimpleList-method Man page
coerce,SimpleList,AssaysInEnv-method Man page
coerce,SimpleList,ShallowSimpleListAssays-method Man page
coerce,SimpleList,SimpleAssays-method Man page
coerce,SummarizedExperiment,ExpressionSet-method Man page
coerce,SummarizedExperiment,RangedSummarizedExperiment-method Man page
colData Man page
colData,SummarizedExperiment-method Man page
colData<- Man page
colData<-,SummarizedExperiment,DataFrame-method Man page
colData<-,SummarizedExperiment,NULL-method Man page
colnames,SummarizedExperiment-method Man page
combineCols Man page
combineCols,SummarizedExperiment-method Man page
combineRows Man page
combineRows,SummarizedExperiment-method Man page
combine_assays_by Source code
coverage Man page
coverage,RangedSummarizedExperiment-method Man page
coverage-methods Man page
create_dummy_matrix Source code
dim,Assays-method Man page
dimnames<-,RangedSummarizedExperiment,list-method Man page
dimnames<-,SummarizedExperiment,NULL-method Man page
dimnames<-,SummarizedExperiment,list-method Man page
disjointBins Man page
disjointBins,RangedSummarizedExperiment-method Man page
distance Man page
distance,ANY,RangedSummarizedExperiment-method Man page
distance,RangedSummarizedExperiment,ANY-method Man page
distance,RangedSummarizedExperiment,RangedSummarizedExperiment-m Man page
distanceToNearest Man page
distanceToNearest,ANY,RangedSummarizedExperiment-method Man page
distanceToNearest,RangedSummarizedExperiment,ANY-method Man page
distanceToNearest,RangedSummarizedExperiment,RangedSummarizedExp Man page
duplicated,RangedSummarizedExperiment-method Man page
elementMetadata,RangedSummarizedExperiment-method Man page
elementMetadata<-,RangedSummarizedExperiment-method Man page
end,RangedSummarizedExperiment-method Man page
end<-,RangedSummarizedExperiment-method Man page
extract_granges_from_se Source code
findOverlaps Man page
findOverlaps,RangedSummarizedExperiment,RangedSummarizedExperime Man page
findOverlaps,RangedSummarizedExperiment,Vector-method Man page
findOverlaps,Vector,RangedSummarizedExperiment-method Man page
findOverlaps-methods Man page
flank Man page
flank,RangedSummarizedExperiment-method Man page
follow Man page
follow,ANY,RangedSummarizedExperiment-method Man page
follow,RangedSummarizedExperiment,ANY-method Man page
follow,RangedSummarizedExperiment,RangedSummarizedExperiment-met Man page
geneRangeMapper Man page Source code
getListElement,Assays-method Man page
getListElement,AssaysInEnv-method Man page
granges,RangedSummarizedExperiment-method Man page
horizontal_slot_names,SummarizedExperiment-method Man page
inflate_matrix_by_column Source code
inflate_matrix_by_row Source code
inter-range-methods Man page
intra-range-methods Man page
is.unsorted,RangedSummarizedExperiment-method Man page
isDisjoint Man page
isDisjoint,RangedSummarizedExperiment-method Man page
length,Assays-method Man page
length,AssaysInEnv-method Man page
length,SummarizedExperiment-method Man page
makeSummarizedExperimentFromDataFrame Man page Source code
makeSummarizedExperimentFromExpressionSet Man page Source code
makeSummarizedExperimentFromLoom Man page Source code
mcols,RangedSummarizedExperiment-method Man page
mcols<-,RangedSummarizedExperiment-method Man page
merge_granges_from_se Source code
naiveRangeMapper Man page Source code
names,Assays-method Man page
names,AssaysInEnv-method Man page
names,RangedSummarizedExperiment-method Man page
names,SummarizedExperiment-method Man page
names<-,Assays-method Man page
names<-,AssaysInEnv-method Man page
names<-,RangedSummarizedExperiment-method Man page
names<-,SummarizedExperiment-method Man page
narrow Man page
narrow,RangedSummarizedExperiment-method Man page
ncol,SummarizedExperiment-method Man page
nearest Man page
nearest,ANY,RangedSummarizedExperiment-method Man page
nearest,RangedSummarizedExperiment,ANY-method Man page
nearest,RangedSummarizedExperiment,RangedSummarizedExperiment-me Man page
nearest-methods Man page
new_RangedSummarizedExperiment Source code
new_SummarizedExperiment Source code
normarg_assays Source code
nrow,SummarizedExperiment-method Man page
order,RangedSummarizedExperiment-method Man page
parallel_slot_names,RangedSummarizedExperiment-method Man page
parallel_slot_names,SummarizedExperiment-method Man page
pcompare,ANY,RangedSummarizedExperiment-method Man page
pcompare,RangedSummarizedExperiment,ANY-method Man page
pcompare,RangedSummarizedExperiment,RangedSummarizedExperiment-m Man page
precede Man page
precede,ANY,RangedSummarizedExperiment-method Man page
precede,RangedSummarizedExperiment,ANY-method Man page
precede,RangedSummarizedExperiment,RangedSummarizedExperiment-me Man page
probeRangeMapper Man page Source code
promoters Man page
promoters,RangedSummarizedExperiment-method Man page
ranges,RangedSummarizedExperiment-method Man page
ranges<-,RangedSummarizedExperiment-method Man page
rank,RangedSummarizedExperiment-method Man page
rbind,Assays-method Man page
rbind,SummarizedExperiment-method Man page
realize,SummarizedExperiment-method Man page
resize Man page
resize,RangedSummarizedExperiment-method Man page
restrict Man page
restrict,RangedSummarizedExperiment-method Man page
rowData Man page
rowData,SummarizedExperiment-method Man page
rowData<- Man page
rowData<-,SummarizedExperiment-method Man page
rowRanges Man page
rowRanges,RangedSummarizedExperiment-method Man page
rowRanges,SummarizedExperiment-method Man page
rowRanges<- Man page
rowRanges<-,RangedSummarizedExperiment,NULL-method Man page
rowRanges<-,SummarizedExperiment,GRangesList-method Man page
rowRanges<-,SummarizedExperiment,GenomicRanges-method Man page
rowRanges<-,SummarizedExperiment,NULL-method Man page
rownames,SummarizedExperiment-method Man page
saveRDS,SummarizedExperiment-method Man page
seqinfo,RangedSummarizedExperiment-method Man page
seqinfo<-,RangedSummarizedExperiment-method Man page
seqnames,RangedSummarizedExperiment-method Man page
setListElement,Assays-method Man page
setListElement,AssaysInEnv-method Man page
shift Man page
shift,RangedSummarizedExperiment-method Man page
show,SummarizedExperiment-method Man page
showAsCell,SummarizedExperiment-method Man page
sort,RangedSummarizedExperiment-method Man page
split,RangedSummarizedExperiment,ANY-method Man page
split,RangedSummarizedExperiment-method Man page
start,RangedSummarizedExperiment-method Man page
start<-,RangedSummarizedExperiment-method Man page
strand,RangedSummarizedExperiment-method Man page
strand<-,RangedSummarizedExperiment,ANY-method Man page
subset,RangedSummarizedExperiment-method Man page
subset,SummarizedExperiment-method Man page
terminators Man page
terminators,RangedSummarizedExperiment-method Man page
trim,RangedSummarizedExperiment-method Man page
updateObject,Assays-method Man page
updateObject,RangedSummarizedExperiment-method Man page
updateObject,SummarizedExperiment-method Man page
vertical_slot_names,SummarizedExperiment-method Man page
width,RangedSummarizedExperiment-method Man page
width<-,RangedSummarizedExperiment-method Man page
Bioconductor/SummarizedExperiment documentation built on Nov. 2, 2024, 8:20 a.m.

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