OutriderDataSet-class: OutriderDataSet class and constructors
In gagneurlab/OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER
OutriderDataSet-class R Documentation
OutriderDataSet class and constructors
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
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
ods <- makeExampleOutriderDataSet()
ods
ods <- makeExampleOutriderDataSet(dataset="Kremer")
ods
gagneurlab/OUTRIDER documentation built on April 19, 2024, 12:20 a.m.
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| OutriderDataSet-class | R Documentation |
OutriderDataSet class and constructors
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
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 |
colData |
Additional to the count data a |
... |
Further arguments can be passed to
|
Value
An OutriderDataSet object.
Author(s)
Christian Mertes mertes@in.tum.de, Felix Brechtmann brechtma@in.tum.de
Examples
ods <- makeExampleOutriderDataSet()
ods
ods <- makeExampleOutriderDataSet(dataset="Kremer")
ods
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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