In drighelli/multiAssayDataScratch:

General

The aim of this file is to provide a schematic organization of the "Bioconductor Experiment" classes in terms of attributes and methods describing them.

The SummarizedExperiment Class

The SummarizedExperiment object is defined in Bioconductor since BioC version 3.2 (R-3.2). It's aim is to flexibly easily provide an instrument for sequencing and microarray data experiments handling.

SummarizedExperiment Refs

1. http://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html

2. https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html

SummarizedExperiment Cheatsheet

\begin{tabular}{lll} \hline Attribute & Class & Description \ \hline assays & list & list of named data matrices \ colData & DataFrame & describes samples (columns) units \ rowData & DataFrame & describes features (rows) units \ \hdashline Other attribute & Class & Description \ \hdashline elementMetadata & DataFrame & describes additional information on the experiment \ metadata & list & list of elementMetadata\ NAMES & character_OR_NULL & NOT CLEAR \

\hline Method & Output & Description \ \hline SummarizedExperiment & SummarizedExperiment & constructor \ assays & list & gets/sets a list of assays \ assay & matrix & gets/sets the first assay \ rowData & DataFrame & gets/sets the rowData structure \ colData & DataFrame & gets/sets the colData structure \ \lbrack & SummarizedExperiment & subsets the object like a matrix/DataFrame\ \$ & DataFrame & operates on the colData columns\ \end{tabular}

The RangedSummarizedExperiment Class

The RagnedSummarizedExperiment class extends the SummarizedExperiment class and is defined in Bioconductor since BioC version 3.2 (R-3.2). It's aim is to provide a more flexible representation of the features in terms of GenomicRanges coordinates.

RangedSummarizedExperiment Refs

1. http://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html

2. https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html

RangedSummarizedExperiment Cheatsheet

\begin{tabular}{lll} \hline Attribute & Class & Description \ \hline rowRanges & GenomicRanges & describes features as genomic coordinates \ \hline Method & Output & Description \ \hline SummarizedExperiment & RangedSummarizedExperiment & constructor (give rowRanges)\ RangedSummarizedExperiment & RangedSummarizedExperiment & constructor \ rowRanges & GenomicRanges & gets/sets the rowRanges structure \ subsetByOverlaps & RangedSummarizedExperiment & subsets the object with overlapped ranges\ \end{tabular}

The SingleCellExperiment Class

The SingleCellExperiment object is defined in Bioconductor since BioC version 3.6 (R-3.4) extending the RangedSummarizedExperiment Bioconductor object.

For simplicity, exception made when necessary, inherited attributes or methods are not reported.

SingleCellExperiment Refs

1. http://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html

2. https://bioconductor.org/packages/release/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html

SingleCellExperiment Cheatsheet

\begin{tabular}{lll} \hline Attribute & Class & Description \ \hline assays & list & list of named data matrices \ colData & DataFrame & describes samples (columns) units \ rowData & DataFrame & describes features (rows) units \ rowRanges & GenomicRanges & describes features as genomic coordinates \ int_colData & DataFrame & as colData, but internal (not for direct access) \ reducedDims & SimpleList & list of matrices representing reduced dimentions of data \ \hdashline Other attribute & Class & Description \ \hdashline elementMetadata & DataFrame & describes additional information on the experiment \ metadata & list & list of elementMetadata\ int_metadata & list & see metadata, but internal (not for direct access) \ int_elementMetadata & DataFrame & see elementMetadata, but internal (not for direct access) \ NAMES & character_OR_NULL & NOT CLEAR \ \hline Method & Output & Description \ \hline SingleCellExperiment & SingleCellExperiment & constructor \ isSpike & logical & gets/sets rows corresponding to spike-in transcripts \ spikeNames & character & the spike-ins in the object \ sizeFactors & numeric & gets/sets the factors (columns) size (based on reads amount) \ clearSizeFactors & SingleCellExperiment & clears size factors and returns the new SingleCellExperiment object \ sizeFactorNames & character & gets/sets the names of the sizeFacors (if present) \ colData & DataFrame & gets/sets the colData structure \ rowData & DataFrame & gets/sets the rowData structure \ rowRanges & GenomicRanges & gets/sets the rowRanges structure \ reducedDim & matrix & gets/sets one element of reducedDims list \ reducedDims & list & gets/sets the reducedDims list \ reducedDimNames & character & gets/sets the reducedDims list names \

\end{tabular}

drighelli/multiAssayDataScratch documentation built on Feb. 12, 2020, 5:27 a.m.