OutriderDataSet-class: OutriderDataSet class and constructors

Description Usage Arguments Value Author(s) Examples

Description

The OutriderDataSet class is designed to store the whole OUTRIDER data set needed for an analysis. It is a subclass of RangedSummarizedExperiment. All calculated values and results are stored as assays or as annotation in the mcols structure provided by the RangedSummarizedExperiment class.

Usage

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OutriderDataSet(se, countData, colData, ...)

Arguments

se

A RangedSummarizedExperiment object or any object which inherits from it and contains a count matrix as the first element in the assay list.

countData

A simple count matrix. If dim names are provided, they have to be unique. This is only used if no se object is provided.

colData

Additional to the count data a DataFrame can be provided to annotate the samples.

...

Further arguments can be passed to DESeqDataSet, which is used to parse the user input and create the initial RangedSummarizedExperiment object.

Value

An OutriderDataSet object.

Author(s)

Christian Mertes mertes@in.tum.de, Felix Brechtmann brechtma@in.tum.de

Examples

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ods <- makeExampleOutriderDataSet()
ods

ods <- makeExampleOutriderDataSet(dataset="Kremer")
ods
   

gagneurlab/OUTRIDER documentation built on Oct. 24, 2020, 6:49 p.m.