API for SummarizedExperiment
SummarizedExperiment container

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_identical_dimnames	Source code
.bind_Assays_objects	Source code
.bind_assays	Source code
.cbind.DataFrame	Source code
.cbind.SummarizedExperiment	Source code
.close	Source code
.close.H5IdComponent	Source code
.close.connection	Source code
.close.list	Source code
.colData	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_assays	Source code
.get_rownames_from_assays	Source code
.loom_make_rownames	Source code
.new_RangedSummarizedExperiment	Source code
.open	Source code
.rbind.SummarizedExperiment	Source code
.read	Source code
.read.H5IdComponent	Source code
.read.connection	Source code
.readIds	Source code
.replace_Assays_subset	Source code
.require	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
KALLISTO_ASSAYS	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
coverage	Man page
coverage,RangedSummarizedExperiment-method	Man page
coverage-methods	Man page
dim,Assays-method	Man page
dim,SummarizedExperiment-method	Man page
dimnames,RangedSummarizedExperiment-method	Man page
dimnames,SummarizedExperiment-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
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
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
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
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_SummarizedExperiment	Source code
normarg_assays	Source code
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
readKallisto	Man page Source code
readKallistoBootstrap	Man page Source code
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
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
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
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