SummarizedExperiment container
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Documentation for package ‘SummarizedExperiment’ version 1.24.0
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A C D E F G H I K L M N O P R S T U V W misc
-- A --
| acbind-method | Assays objects |
| arbind-method | Assays objects |
| assay | SummarizedExperiment objects |
| assay-method | SummarizedExperiment objects |
| assay<- | SummarizedExperiment objects |
| assay<--method | SummarizedExperiment objects |
| assayNames | SummarizedExperiment objects |
| assayNames-method | SummarizedExperiment objects |
| assayNames<- | SummarizedExperiment objects |
| assayNames<--method | SummarizedExperiment objects |
| Assays | Assays objects |
| assays | SummarizedExperiment objects |
| Assays-class | Assays objects |
| assays-method | SummarizedExperiment objects |
| assays<- | SummarizedExperiment objects |
| assays<--method | SummarizedExperiment objects |
| AssaysInEnv | Assays objects |
| AssaysInEnv-class | Assays objects |
| Assays_OR_NULL | SummarizedExperiment objects |
| Assays_OR_NULL-class | SummarizedExperiment objects |
-- C --
| cbind-method | Assays objects |
| cbind-method | SummarizedExperiment objects |
| class:Assays | Assays objects |
| class:AssaysInEnv | Assays objects |
| class:Assays_OR_NULL | SummarizedExperiment objects |
| class:RangedSummarizedExperiment | RangedSummarizedExperiment objects |
| class:ShallowData | Assays objects |
| class:ShallowSimpleListAssays | Assays objects |
| class:SimpleAssays | Assays objects |
| class:SummarizedExperiment | SummarizedExperiment objects |
| coerce-method | Assays objects |
| coerce-method | RangedSummarizedExperiment objects |
| coerce-method | Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa |
| colData | SummarizedExperiment objects |
| colData-method | SummarizedExperiment objects |
| colData<- | SummarizedExperiment objects |
| colData<--method | SummarizedExperiment objects |
| combineCols | SummarizedExperiment objects |
| combineCols-method | SummarizedExperiment objects |
| combineRows | SummarizedExperiment objects |
| combineRows-method | SummarizedExperiment objects |
| Compare-method | 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 | SummarizedExperiment objects |
| dimnames-method | RangedSummarizedExperiment objects |
| dimnames-method | SummarizedExperiment objects |
| dimnames<--method | RangedSummarizedExperiment objects |
| dimnames<--method | SummarizedExperiment 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 |
-- 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 |
| getListElement-method | Assays objects |
| granges-method | RangedSummarizedExperiment objects |
-- H --
| horizontal_slot_names-method | SummarizedExperiment objects |
-- I --
| inter-range-methods | Inter range transformations of a RangedSummarizedExperiment object |
| intra-range-methods | Intra range transformations of a RangedSummarizedExperiment object |
| is.unsorted-method | RangedSummarizedExperiment objects |
| 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 | SummarizedExperiment objects |
-- M --
| makeSummarizedExperimentFromDataFrame | Make a RangedSummarizedExperiment from a data.frame or DataFrame |
| makeSummarizedExperimentFromExpressionSet | Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa |
| makeSummarizedExperimentFromLoom | Make a SummarizedExperiment from a '.loom' hdf5 file |
| 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 | SummarizedExperiment objects |
| names<--method | Assays objects |
| names<--method | RangedSummarizedExperiment objects |
| names<--method | SummarizedExperiment 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 |
-- P --
| parallel_slot_names-method | RangedSummarizedExperiment objects |
| parallel_slot_names-method | SummarizedExperiment objects |
| pcompare-method | RangedSummarizedExperiment objects |
| 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 | SummarizedExperiment objects |
| readKallisto | Input kallisto or kallisto bootstrap results. |
| readKallistoBootstrap | Input kallisto or kallisto bootstrap results. |
| realize-method | SummarizedExperiment 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 |
| rowData | SummarizedExperiment objects |
| rowData-method | SummarizedExperiment objects |
| rowData<- | SummarizedExperiment objects |
| rowData<--method | SummarizedExperiment objects |
| 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 |
| setListElement-method | Assays objects |
| ShallowData | Assays objects |
| ShallowData-class | Assays 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 | SummarizedExperiment objects |
| showAsCell-method | SummarizedExperiment objects |
| SimpleAssays | Assays objects |
| SimpleAssays-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 |
| subset-method | SummarizedExperiment objects |
| SummarizedExperiment | RangedSummarizedExperiment objects |
| SummarizedExperiment-class | SummarizedExperiment objects |
-- T --
| trim-method | Intra range transformations of a RangedSummarizedExperiment object |
-- U --
| updateObject-method | Assays objects |
| updateObject-method | RangedSummarizedExperiment objects |
| updateObject-method | SummarizedExperiment objects |
-- V --
| vertical_slot_names-method | SummarizedExperiment objects |
-- W --
| width-method | RangedSummarizedExperiment objects |
| width<--method | RangedSummarizedExperiment objects |
-- misc --
| $-method | SummarizedExperiment objects |
| $<--method | SummarizedExperiment objects |
| [-method | Assays objects |
| [-method | SummarizedExperiment objects |
| [<--method | Assays objects |
| [<--method | SummarizedExperiment objects |
| [[-method | SummarizedExperiment objects |
| [[<--method | SummarizedExperiment objects |