Package: ExperimentSubset 1.17.0
Irzam Sarfraz
ExperimentSubset: Manages subsets of data with Bioconductor Experiment objects
Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for one or more matrix-like assays along with the associated row and column data. Often only a subset of the original data is needed for down-stream analysis. For example, filtering out poor quality samples will require excluding some columns before analysis. The ExperimentSubset object is a container to efficiently manage different subsets of the same data without having to make separate objects for each new subset.
Authors:
ExperimentSubset_1.17.0.tar.gz
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ExperimentSubset.pdf |ExperimentSubset.html✨
ExperimentSubset/json (API)
NEWS
| # Install 'ExperimentSubset' in R: |
| install.packages('ExperimentSubset', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:ExperimentSubset-1.15.0(bioc 3.20)ExperimentSubset-1.14.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
infrastructuresoftwaredataimportdatarepresentation
Last updated 23 days agofrom:48fa54289e. Checks:OK: 2 NOTE: 4 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | OK | Oct 31 2024 |
| R-4.3-mac | ERROR | Oct 31 2024 |
Exports:createSubsetExperimentSubsetgetSubsetAssayreducedDimNamesreducedDimNames<-reducedDims<-setSubsetAssaysubsetAssayCountsubsetAssayNamessubsetColDatasubsetColData<-subsetColLinkssubsetColnamessubsetColnames<-subsetCountsubsetDimsubsetNamessubsetParentsubsetRowDatasubsetRowData<-subsetRowLinkssubsetRownamessubsetRownames<-subsetSpatialCoordssubsetSpatialDatasubsetSpatialData<-subsetSummary
Dependencies:abindapeaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrfansifastmapfilelockformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelazyevallifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslpillarpkgconfigplogrpurrrR6RcpprjsonrlangRSQLiteS4ArraysS4VectorsSingleCellExperimentsnowSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimentUCSC.utilsutf8vctrswithrXVectoryulab.utilszlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| AssaySubset constructor | AssaySubset |
| An S4 class to manage subset representation. | .AssaySubset AssaySubset-class |
| Subset creation method for ExperimentSubset objects | createSubset createSubset,SubsetRangedSummarizedExperiment-method createSubset,SubsetSingleCellExperiment-method createSubset,SubsetSpatialExperiment-method createSubset,SubsetSummarizedExperiment-method createSubset,SubsetTreeSummarizedExperiment-method |
| ExperimentSubset constructor | ExperimentSubset |
| Get subset assay from an 'ExperimentSubset' object. | getSubsetAssay getSubsetAssay,SubsetRangedSummarizedExperiment,character-method getSubsetAssay,SubsetSingleCellExperiment,character-method getSubsetAssay,SubsetSpatialExperiment,character-method getSubsetAssay,SubsetSummarizedExperiment,character-method getSubsetAssay,SubsetTreeSummarizedExperiment,character-method |
| reducedDimNames | reducedDimNames reducedDimNames,ANY-method |
| reducedDimNames<- | reducedDimNames<- reducedDimNames<-,ANY-method |
| reducedDims<- | reducedDims<- |
| reducedDims<- | reducedDims<-,ANY-method |
| Method for storing new assays inside subsets in ExperimentSubset objects | setSubsetAssay setSubsetAssay,SubsetRangedSummarizedExperiment,character,ANY,character-method setSubsetAssay,SubsetSingleCellExperiment,character,ANY,character-method setSubsetAssay,SubsetSpatialExperiment,character,ANY,character-method setSubsetAssay,SubsetSummarizedExperiment,character,ANY,character-method setSubsetAssay,SubsetTreeSummarizedExperiment,character,ANY,character-method |
| Count method for subset assays in ExperimentSubset objects | subsetAssayCount subsetAssayCount,SubsetRangedSummarizedExperiment-method subsetAssayCount,SubsetSingleCellExperiment-method subsetAssayCount,SubsetSpatialExperiment-method subsetAssayCount,SubsetSummarizedExperiment-method subsetAssayCount,SubsetTreeSummarizedExperiment-method |
| Name retrieval method for all subset assays in ExperimentSubset objects | subsetAssayNames subsetAssayNames,SubsetRangedSummarizedExperiment-method subsetAssayNames,SubsetSingleCellExperiment-method subsetAssayNames,SubsetSpatialExperiment-method subsetAssayNames,SubsetSummarizedExperiment-method subsetAssayNames,SubsetTreeSummarizedExperiment-method |
| Accessor method for colData from subsets in ExperimentSubset objects | subsetColData subsetColData,SubsetRangedSummarizedExperiment,character-method subsetColData,SubsetSingleCellExperiment,character-method subsetColData,SubsetSpatialExperiment,character-method subsetColData,SubsetSummarizedExperiment,character-method subsetColData,SubsetTreeSummarizedExperiment,character-method subsetColData<- subsetColData<-,SubsetRangedSummarizedExperiment,character,DataFrame-method subsetColData<-,SubsetSingleCellExperiment,character,DataFrame-method subsetColData<-,SubsetSpatialExperiment,character,DataFrame-method subsetColData<-,SubsetSummarizedExperiment,character,DataFrame-method subsetColData<-,SubsetTreeSummarizedExperiment,character,DataFrame-method |
| Accessor method for colLinks from subsets in ExperimentSubset objects | subsetColLinks subsetColLinks,SubsetTreeSummarizedExperiment,character-method |
| subsetColnames | subsetColnames subsetColnames,SubsetRangedSummarizedExperiment,character-method subsetColnames,SubsetSingleCellExperiment,character-method subsetColnames,SubsetSpatialExperiment,character-method subsetColnames,SubsetSummarizedExperiment,character-method subsetColnames,SubsetTreeSummarizedExperiment,character-method subsetColnames<- subsetColnames<-,SubsetRangedSummarizedExperiment,character-method subsetColnames<-,SubsetSingleCellExperiment,character-method subsetColnames<-,SubsetSpatialExperiment,character-method subsetColnames<-,SubsetSummarizedExperiment,character-method subsetColnames<-,SubsetTreeSummarizedExperiment,character-method |
| Subset count method for ExperimentSubset objects | subsetCount subsetCount,SubsetRangedSummarizedExperiment-method subsetCount,SubsetSingleCellExperiment-method subsetCount,SubsetSpatialExperiment-method subsetCount,SubsetSummarizedExperiment-method subsetCount,SubsetTreeSummarizedExperiment-method |
| Get dimensions of subsets in ExperimentSubset objects | subsetDim subsetDim,SubsetRangedSummarizedExperiment,character-method subsetDim,SubsetSingleCellExperiment,character-method subsetDim,SubsetSpatialExperiment,character-method subsetDim,SubsetSummarizedExperiment,character-method subsetDim,SubsetTreeSummarizedExperiment,character-method |
| Get names of only the subsets in ExperimentSubset objects | subsetNames subsetNames,SubsetRangedSummarizedExperiment-method subsetNames,SubsetSingleCellExperiment-method subsetNames,SubsetSpatialExperiment-method subsetNames,SubsetSummarizedExperiment-method subsetNames,SubsetTreeSummarizedExperiment-method |
| Subset parent hierarchy retrieval method for ExperimentSubset objects | subsetParent subsetParent,SubsetRangedSummarizedExperiment-method subsetParent,SubsetSingleCellExperiment-method subsetParent,SubsetSpatialExperiment-method subsetParent,SubsetSummarizedExperiment-method subsetParent,SubsetTreeSummarizedExperiment-method |
| An S4 class for 'RangedSummarizedExperiment' objects with added support for subsets. | .SubsetRangedSummarizedExperiment SubsetRangedSummarizedExperiment-class |
| Accessor method for rowData from subsets in ExperimentSubset objects | subsetRowData subsetRowData,SubsetRangedSummarizedExperiment,character-method subsetRowData,SubsetSingleCellExperiment,character-method subsetRowData,SubsetSpatialExperiment,character-method subsetRowData,SubsetSummarizedExperiment,character-method subsetRowData,SubsetTreeSummarizedExperiment,character-method subsetRowData<- subsetRowData<-,SubsetRangedSummarizedExperiment,character,DataFrame-method subsetRowData<-,SubsetSingleCellExperiment,character,DataFrame-method subsetRowData<-,SubsetSpatialExperiment,character,DataFrame-method subsetRowData<-,SubsetSummarizedExperiment,character,DataFrame-method subsetRowData<-,SubsetTreeSummarizedExperiment,character,DataFrame-method |
| Accessor method for rowLinks from subsets in ExperimentSubset objects | subsetRowLinks subsetRowLinks,SubsetTreeSummarizedExperiment,character-method |
| subsetRownames | subsetRownames subsetRownames,SubsetRangedSummarizedExperiment,character-method subsetRownames,SubsetSingleCellExperiment,character-method subsetRownames,SubsetSpatialExperiment,character-method subsetRownames,SubsetSummarizedExperiment,character-method subsetRownames,SubsetTreeSummarizedExperiment,character-method subsetRownames<- subsetRownames<-,SubsetRangedSummarizedExperiment,character-method subsetRownames<-,SubsetSingleCellExperiment,character-method subsetRownames<-,SubsetSpatialExperiment,character-method subsetRownames<-,SubsetSummarizedExperiment,character-method subsetRownames<-,SubsetTreeSummarizedExperiment,character-method |
| An S4 class for 'SingleCellExperiment' objects with added support for subsets. | .SubsetSingleCellExperiment SubsetSingleCellExperiment-class |
| Accessor method for spatialCoords from subsets in ExperimentSubset objects | subsetSpatialCoords subsetSpatialCoords,SubsetSpatialExperiment,character-method |
| Accessor method for spatialData from subsets in ExperimentSubset objects | subsetSpatialData subsetSpatialData,SubsetSpatialExperiment,character-method subsetSpatialData<- subsetSpatialData<-,SubsetSpatialExperiment,character,data.frame-method |
| An S4 class for 'SpatialExperiment' objects with added support for subsets. | .SubsetSpatialExperiment SubsetSpatialExperiment-class |
| An S4 class for 'SummarizedExperiment' objects with added support for subsets. | .SubsetSummarizedExperiment SubsetSummarizedExperiment-class |
| Method for displaying 'child-parent' link structure of subsets in ExperimentSubset objects | subsetSummary subsetSummary,SubsetRangedSummarizedExperiment-method subsetSummary,SubsetSingleCellExperiment-method subsetSummary,SubsetSpatialExperiment-method subsetSummary,SubsetSummarizedExperiment-method subsetSummary,SubsetTreeSummarizedExperiment-method |
| An S4 class for 'TreeSummarizedExperiment' objects with added support for subsets. | .SubsetTreeSummarizedExperiment SubsetTreeSummarizedExperiment-class |
