Package: ExperimentSubset 1.23.0

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:Irzam Sarfraz [aut, cre], Muhammad Asif [aut, ths], Joshua D. Campbell [aut]

ExperimentSubset_1.23.0.tar.gz
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ExperimentSubset_1.23.0.tgz(r-4.6-any)ExperimentSubset_1.23.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ExperimentSubset/json (API)

# Install 'ExperimentSubset' in R:

install.packages('ExperimentSubset', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:ExperimentSubset-1.23.0(bioc 3.24)ExperimentSubset-1.22.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

infrastructure software dataimport datarepresentation

4.00 score 8 scripts 27 exports 78 dependencies

Last updated from:6186a5d5c4. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	252
linux-devel-x86_64	NOTE	433
source / vignettes	OK	407
linux-release-x86_64	NOTE	451
macos-release-arm64	NOTE	273
macos-oldrel-arm64	NOTE	193
windows-devel	NOTE	1184
windows-release	NOTE	1117
windows-oldrel	NOTE	1127
wasm-release	OK	246

Exports:createSubset ExperimentSubset getSubsetAssay reducedDimNames reducedDimNames<-reducedDims<-setSubsetAssay subsetAssayCount subsetAssayNames subsetColData subsetColData<-subsetColLinks subsetColnames subsetColnames<-subsetCount subsetDim subsetNames subsetParent subsetRowData subsetRowData<-subsetRowLinks subsetRownames subsetRownames<-subsetSpatialCoords subsetSpatialData subsetSpatialData<-subsetSummary

Dependencies:abind ape askpass BH Biobase BiocFileCache BiocGenerics BiocParallel Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl DBI dbplyr DelayedArray digest dplyr fastmap filelock formatR fs futile.logger futile.options generics GenomicRanges glue httr2 IRanges jsonlite lambda.r lattice lazyeval lifecycle magick magrittr Matrix MatrixGenerics matrixStats memoise nlme openssl pillar pkgconfig purrr R6 rappdirs Rcpp rjson rlang RSQLite S4Arrays S4Vectors Seqinfo SingleCellExperiment snow SparseArray SpatialExperiment stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tidytree treeio TreeSummarizedExperiment utf8 vctrs withr XVector yulab.utils

ExperimentSubset: Manages subsets of data with Bioconductor Experiment objects

Rendered fromExperimentSubset.Rmdusingknitr::rmarkdown

Last update: 2021-03-06
Started: 2020-08-17

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

Package: ExperimentSubset 1.23.0

ExperimentSubset: Manages subsets of data with Bioconductor Experiment objects

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