Package: RaggedExperiment 1.29.0

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:Martin Morgan [aut], Marcel Ramos [aut, cre], Lydia King [ctb]

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Bug tracker:https://github.com/bioconductor/raggedexperiment/issues

On BioConductor:RaggedExperiment-1.29.0(bioc 3.20)RaggedExperiment-1.28.0(bioc 3.19)

bioconductor-package

29 exports 2.92 score 29 dependencies 13 dependents 1 mentions

Last updated 2 months agofrom:5c3ad3ba83

Exports:as.data.frameas.listassayassayNamesassayscoercecolDatacolData<-compactAssaycompactSummarizedExperimentdisjoinAssaydisjoinSummarizedExperimentmcolsmcols<-overlapsAnyqreduceAssayqreduceSummarizedExperimentRaggedExperimentrowDatarowData<-rowRangesrowRanges<-seqinfoseqinfo<-showsparseAssaysparseSummarizedExperimentsubsetsubsetByOverlaps

Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocGenericscrayoncurlDelayedArrayGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc