SummarizedExperiment container

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Documentation for package ‘SummarizedExperiment’ version 1.0.0

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A C D E F G I K L M N O P R S T U W misc

-- A --

assay SummarizedExperiment0 objects
assay-method SummarizedExperiment0 objects
assay<- SummarizedExperiment0 objects
assay<--method SummarizedExperiment0 objects
assayNames SummarizedExperiment0 objects
assayNames-method SummarizedExperiment0 objects
assayNames<- SummarizedExperiment0 objects
assayNames<--method SummarizedExperiment0 objects
Assays Assays objects
assays SummarizedExperiment0 objects
Assays-class Assays objects
assays-method SummarizedExperiment0 objects
assays<- SummarizedExperiment0 objects
assays<--method SummarizedExperiment0 objects
AssaysInEnv Assays objects
AssaysInEnv-class Assays objects

-- C --

cbind-method Assays objects
cbind-method SummarizedExperiment0 objects
class:Assays Assays objects
class:AssaysInEnv Assays objects
class:RangedSummarizedExperiment RangedSummarizedExperiment objects
class:ShallowSimpleListAssays Assays objects
class:SimpleListAssays Assays objects
class:SummarizedExperiment0 SummarizedExperiment0 objects
coerce-method Assays objects
coerce-method RangedSummarizedExperiment objects
coerce-method Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa
colData SummarizedExperiment0 objects
colData-method SummarizedExperiment0 objects
colData<- SummarizedExperiment0 objects
colData<--method SummarizedExperiment0 objects
Compare-method RangedSummarizedExperiment objects
compare-method RangedSummarizedExperiment objects
countOverlaps Finding overlapping ranges in RangedSummarizedExperiment objects
countOverlaps-method Finding overlapping ranges in RangedSummarizedExperiment objects
coverage Coverage of a RangedSummarizedExperiment object
coverage-method Coverage of a RangedSummarizedExperiment object
coverage-methods Coverage of a RangedSummarizedExperiment object

-- D --

dim-method Assays objects
dim-method SummarizedExperiment0 objects
dimnames-method RangedSummarizedExperiment objects
dimnames-method SummarizedExperiment0 objects
dimnames<--method RangedSummarizedExperiment objects
dimnames<--method SummarizedExperiment0 objects
disjointBins Inter range transformations of a RangedSummarizedExperiment object
disjointBins-method Inter range transformations of a RangedSummarizedExperiment object
distance Finding the nearest range neighbor in RangedSummarizedExperiment objects
distance-method Finding the nearest range neighbor in RangedSummarizedExperiment objects
distanceToNearest Finding the nearest range neighbor in RangedSummarizedExperiment objects
distanceToNearest-method Finding the nearest range neighbor in RangedSummarizedExperiment objects
duplicated-method RangedSummarizedExperiment objects

-- E --

elementMetadata-method RangedSummarizedExperiment objects
elementMetadata<--method RangedSummarizedExperiment objects
end-method RangedSummarizedExperiment objects
end<--method RangedSummarizedExperiment objects
exptData-method SummarizedExperiment0 objects
exptData<--method SummarizedExperiment0 objects
extractROWS-method SummarizedExperiment0 objects

-- F --

findOverlaps Finding overlapping ranges in RangedSummarizedExperiment objects
findOverlaps-method Finding overlapping ranges in RangedSummarizedExperiment objects
findOverlaps-methods Finding overlapping ranges in RangedSummarizedExperiment objects
flank Intra range transformations of a RangedSummarizedExperiment object
flank-method Intra range transformations of a RangedSummarizedExperiment object
follow Finding the nearest range neighbor in RangedSummarizedExperiment objects
follow-method Finding the nearest range neighbor in RangedSummarizedExperiment objects

-- G --

geneRangeMapper Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa
granges-method RangedSummarizedExperiment objects

-- I --

inter-range-methods Inter range transformations of a RangedSummarizedExperiment object
intra-range-methods Intra range transformations of a RangedSummarizedExperiment object
isDisjoint Inter range transformations of a RangedSummarizedExperiment object
isDisjoint-method Inter range transformations of a RangedSummarizedExperiment object

-- K --

KALLISTO_ASSAYS Input kallisto or kallisto bootstrap results.

-- L --

length-method Assays objects
length-method SummarizedExperiment0 objects

-- M --

makeSummarizedExperimentFromExpressionSet Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa
mcols-method RangedSummarizedExperiment objects
mcols<--method RangedSummarizedExperiment objects

-- N --

naiveRangeMapper Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa
names-method Assays objects
names-method RangedSummarizedExperiment objects
names-method SummarizedExperiment0 objects
names<--method Assays objects
names<--method RangedSummarizedExperiment objects
names<--method SummarizedExperiment0 objects
narrow Intra range transformations of a RangedSummarizedExperiment object
narrow-method Intra range transformations of a RangedSummarizedExperiment object
nearest Finding the nearest range neighbor in RangedSummarizedExperiment objects
nearest-method Finding the nearest range neighbor in RangedSummarizedExperiment objects
nearest-methods Finding the nearest range neighbor in RangedSummarizedExperiment objects

-- O --

order-method RangedSummarizedExperiment objects
overlapsAny Finding overlapping ranges in RangedSummarizedExperiment objects
overlapsAny-method Finding overlapping ranges in RangedSummarizedExperiment objects

-- P --

precede Finding the nearest range neighbor in RangedSummarizedExperiment objects
precede-method Finding the nearest range neighbor in RangedSummarizedExperiment objects
probeRangeMapper Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa
promoters Intra range transformations of a RangedSummarizedExperiment object
promoters-method Intra range transformations of a RangedSummarizedExperiment object

-- R --

RangedSummarizedExperiment RangedSummarizedExperiment objects
RangedSummarizedExperiment-class RangedSummarizedExperiment objects
ranges-method RangedSummarizedExperiment objects
ranges<--method RangedSummarizedExperiment objects
rank-method RangedSummarizedExperiment objects
rbind-method Assays objects
rbind-method SummarizedExperiment0 objects
readKallisto Input kallisto or kallisto bootstrap results.
readKallistoBootstrap Input kallisto or kallisto bootstrap results.
replaceROWS-method SummarizedExperiment0 objects
resize Intra range transformations of a RangedSummarizedExperiment object
resize-method Intra range transformations of a RangedSummarizedExperiment object
restrict Intra range transformations of a RangedSummarizedExperiment object
restrict-method Intra range transformations of a RangedSummarizedExperiment object
rowRanges RangedSummarizedExperiment objects
rowRanges-method RangedSummarizedExperiment objects
rowRanges<- RangedSummarizedExperiment objects
rowRanges<--method RangedSummarizedExperiment objects

-- S --

seqinfo-method RangedSummarizedExperiment objects
seqinfo<--method RangedSummarizedExperiment objects
seqnames-method RangedSummarizedExperiment objects
ShallowSimpleListAssays Assays objects
ShallowSimpleListAssays-class Assays objects
shift Intra range transformations of a RangedSummarizedExperiment object
shift-method Intra range transformations of a RangedSummarizedExperiment object
show-method SummarizedExperiment0 objects
SimpleListAssays Assays objects
SimpleListAssays-class Assays objects
sort-method RangedSummarizedExperiment objects
split-method RangedSummarizedExperiment objects
start-method RangedSummarizedExperiment objects
start<--method RangedSummarizedExperiment objects
strand-method RangedSummarizedExperiment objects
strand<--method RangedSummarizedExperiment objects
subset-method RangedSummarizedExperiment objects
subsetByOverlaps Finding overlapping ranges in RangedSummarizedExperiment objects
subsetByOverlaps-method Finding overlapping ranges in RangedSummarizedExperiment objects
SummarizedExperiment RangedSummarizedExperiment objects
SummarizedExperiment-method RangedSummarizedExperiment objects
SummarizedExperiment0 SummarizedExperiment0 objects
SummarizedExperiment0-class SummarizedExperiment0 objects

-- T --

trim-method Intra range transformations of a RangedSummarizedExperiment object

-- U --

updateObject-method RangedSummarizedExperiment objects

-- W --

width-method RangedSummarizedExperiment objects
width<--method RangedSummarizedExperiment objects

-- misc --

$-method SummarizedExperiment0 objects
$<--method SummarizedExperiment0 objects
[-method Assays objects
[-method SummarizedExperiment0 objects
[<--method Assays objects
[<--method SummarizedExperiment0 objects
[[-method Assays objects
[[-method SummarizedExperiment0 objects
[[<--method Assays objects
[[<--method SummarizedExperiment0 objects