DENBTest: Perform negative binomial exact test for differential...
In sunlightwang/SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
Description
Perform negative binomial exact test for differential expression - a modified version of nbinomTest in DESeq package.
Usage
1
DENBTest(dds)
Arguments
dds
A DESeqDataSet object with size factors and dispersion parameters estimated. Recommended to take the output of runDESeq.
Value
A data frame of the test results. Information contains mean expression values, NB-statistics, (log) fold-changes, p-values, and adjusted p-values.
Author(s)
Xi Wang, xi.wang@newcastle.edu.au
References
Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data, Genome Biol, 11, R106.
See Also
Examples
1
2
3
4
5
6
data(RCS_example, package="SeqGSEA")
geneCounts <- getGeneCount(RCS_example)
label <- label(RCS_example)
DEG <- runDESeq(geneCounts, label)
DEGres <- DENBTest(DEG)
head(DEGres)
sunlightwang/SeqGSEA documentation built on Dec. 5, 2020, 5:52 p.m.
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Description Usage Arguments Value Author(s) References See Also Examples
Description
Perform negative binomial exact test for differential expression - a modified version of nbinomTest in DESeq package.
Usage
1 | DENBTest(dds)
|
Arguments
dds |
A DESeqDataSet object with size factors and dispersion parameters estimated. Recommended to take the output of |
Value
A data frame of the test results. Information contains mean expression values, NB-statistics, (log) fold-changes, p-values, and adjusted p-values.
Author(s)
Xi Wang, xi.wang@newcastle.edu.au
References
Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data, Genome Biol, 11, R106.
See Also
Examples
1 2 3 4 5 6 | data(RCS_example, package="SeqGSEA")
geneCounts <- getGeneCount(RCS_example)
label <- label(RCS_example)
DEG <- runDESeq(geneCounts, label)
DEGres <- DENBTest(DEG)
head(DEGres)
|
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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