consensusClustersDESeq2: Export _consensus cluster_ expression data for DESeq2...
In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Description
Usage
Arguments
Author(s)
See Also
Examples
Description
Creates a DESeqDataSet using the consensus cluster expression
data in the experiment slot consensusClusters and the sample metadata
of the CAGEexp object. The formula must be built using factors
already present in the sample metadata.
Usage
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consensusClustersDESeq2(object, design)
## S4 method for signature 'CAGEset'
consensusClustersDESeq2(object, design)
## S4 method for signature 'CAGEexp'
consensusClustersDESeq2(object, design)
Arguments
object
A CAGEexp object.
design
A formula for the DESeq2 analysis.
Author(s)
Charles Plessy
See Also
DESeqDataSet in the DESeq2 package.
Other CAGEr clusters functions: CTSSclusteringMethod,
CTSScumulativesTagClusters,
CustomConsensusClusters,
aggregateTagClusters,
clusterCTSS,
consensusClustersGR,
cumulativeCTSSdistribution,
plotInterquantileWidth,
quantilePositions,
tagClusters
Examples
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exampleCAGEexp$group <- c("a", "a", "b", "b", "a")
consensusClustersDESeq2(exampleCAGEexp, ~group)
CAGEr documentation built on Jan. 17, 2021, 2 a.m.
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Description Usage Arguments Author(s) See Also Examples
Description
Creates a DESeqDataSet using the consensus cluster expression
data in the experiment slot consensusClusters and the sample metadata
of the CAGEexp object. The formula must be built using factors
already present in the sample metadata.
Usage
1 2 3 4 5 6 7 | consensusClustersDESeq2(object, design)
## S4 method for signature 'CAGEset'
consensusClustersDESeq2(object, design)
## S4 method for signature 'CAGEexp'
consensusClustersDESeq2(object, design)
|
Arguments
object |
A CAGEexp object. |
design |
A formula for the DESeq2 analysis. |
Author(s)
Charles Plessy
See Also
DESeqDataSet in the DESeq2 package.
Other CAGEr clusters functions: CTSSclusteringMethod,
CTSScumulativesTagClusters,
CustomConsensusClusters,
aggregateTagClusters,
clusterCTSS,
consensusClustersGR,
cumulativeCTSSdistribution,
plotInterquantileWidth,
quantilePositions,
tagClusters
Examples
1 2 | exampleCAGEexp$group <- c("a", "a", "b", "b", "a")
consensusClustersDESeq2(exampleCAGEexp, ~group)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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