The RangedSummarizedExperiment class is a matrix-like container where rows represent ranges of interest (as a GRanges or GRangesList object) and columns represent samples (with sample data summarized as a DataFrame). A RangedSummarizedExperiment contains one or more assays, each represented by a matrix-like object of numeric or other mode.
The SummarizedExperiment class is a matrix-like container where rows represent features of interest (e.g. genes, transcripts, exons, etc...) and columns represent samples (with sample data summarized as a DataFrame). A SummarizedExperiment object contains one or more assays, each represented by a matrix-like object of numeric or other mode.
This man page documents the nearest methods and family (i.e. precede, follow, distance, and distanceToNearest methods) for RangedSummarizedExperiment objects.
readKallisto inputs several kallisto output files into a single SummarizedExperiment instance, with rows corresponding to estimated transcript abundance and columns to samples. readKallistoBootstrap inputs kallisto bootstrap replicates of a single sample into a matrix of transcript x bootstrap abundance estimates.
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