Package: RaggedExperiment 1.31.1
Marcel Ramos
RaggedExperiment: Representation of Sparse Experiments and Assays Across Samples
This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset.
Authors:
RaggedExperiment_1.31.1.tar.gz
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RaggedExperiment_1.31.1.tgz(r-4.4-any)RaggedExperiment_1.31.1.tgz(r-4.3-any)
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RaggedExperiment.pdf |RaggedExperiment.html✨
RaggedExperiment/json (API)
NEWS
| # Install 'RaggedExperiment' in R: |
| install.packages('RaggedExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/raggedexperiment/issues
On BioConductor:RaggedExperiment-1.31.1(bioc 3.21)RaggedExperiment-1.30.0(bioc 3.20)
infrastructuredatarepresentationcopynumbercore-packagedata-structuremutations
Last updated 1 months agofrom:3c81b9a801. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 23 2024 |
| R-4.5-win | OK | Nov 23 2024 |
| R-4.5-linux | OK | Dec 23 2024 |
| R-4.4-win | NOTE | Nov 23 2024 |
| R-4.4-mac | NOTE | Dec 23 2024 |
| R-4.3-win | NOTE | Nov 23 2024 |
| R-4.3-mac | NOTE | Dec 23 2024 |
Exports:as.data.frameas.listassayassayNamesassayscoercecolDatacolData<-compactAssaycompactSummarizedExperimentdisjoinAssaydisjoinSummarizedExperimentmcolsmcols<-overlapsAnyqreduceAssayqreduceSummarizedExperimentRaggedExperimentrowDatarowData<-rowRangesrowRanges<-seqinfoseqinfo<-showsparseAssaysparseSummarizedExperimentsubsetsubsetByOverlaps
Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocGenericscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| RaggedExperiment: Range-based data representation package | RaggedExperiment-package |
| Create simplified representation of ragged assay data. | assay-functions compactAssay disjoinAssay qreduceAssay sparseAssay |
| RaggedExperiment objects | $,RaggedExperiment-method as.data.frame,RaggedExperiment-method as.list,RaggedExperiment-method assay,RaggedExperiment,ANY-method assay,RaggedExperiment,missing-method assayNames,RaggedExperiment-method assays,RaggedExperiment-method class:RaggedExperiment coerce,GRangesList,RaggedExperiment-method coerce,RaggedExperiment,GRangesList-method colData,RaggedExperiment-method colData<-,RaggedExperiment,DataFrame-method dim,RaggedExperiment-method dimnames,RaggedExperiment-method dimnames<-,RaggedExperiment,ANY-method dimnames<-,RaggedExperiment,list-method length,RaggedExperiment-method mcols,RaggedExperiment-method mcols<-,RaggedExperiment-method overlapsAny,RaggedExperiment,Vector-method RaggedExperiment RaggedExperiment-class rowData,RaggedExperiment-method rowData<-,RaggedExperiment-method rowRanges,RaggedExperiment-method rowRanges<-,RaggedExperiment,GRanges-method seqinfo,RaggedExperiment-method seqinfo<-,RaggedExperiment-method show,RaggedExperiment-method subset,RaggedExperiment-method subsetByOverlaps,RaggedExperiment,Vector-method [,RaggedExperiment,ANY,ANY,ANY-method |
| Create SummarizedExperiment representations by transforming ragged assays to rectangular form. | coerce,dgCMatrix,RaggedExperiment-method coerce-RaggedExperiment compactSummarizedExperiment disjoinSummarizedExperiment qreduceSummarizedExperiment sparseSummarizedExperiment |
