DENBStat4GSEA: Calculate NB-statistics quantifying differential expression...

In sunlightwang/SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Description

Calculate NB-statistics quantifying differential expression between two groups of samples compared. The results will be used for GSEA run. Comparing with DENBTest, this function will not calculate NB test p-values.

This function only works with two-group comparison.

Usage

DENBStat4GSEA(dds)

Arguments

dds	A DESeqDataSet object with size factors and dispersion parameters estimated. Recommended to take the output of runDESeq.

Value

A data frame containing each gene's expression means and variances in each group, and each gene's DE NB-statistics.

Note

The results with the output of DENBStatPermut4GSEA can also be used to run DEpermutePval.

Author(s)

Xi Wang, [e-mail]

References

Xi Wang and Murray J. Cairns (2013). Gene Set Enrichment Analysis of RNA-Seq Data: Integrating Differential Expression and Splicing. BMC Bioinformatics, 14(Suppl 5):S16.

See Also

DENBTest, runDESeq, DENBStatPermut4GSEA

Examples

data(RCS_example, package="SeqGSEA")
geneCounts <- getGeneCount(RCS_example)
label <- label(RCS_example)
DEG <- runDESeq(geneCounts, label)
DEGres <- DENBStat4GSEA(DEG)
head(DEGres)

sunlightwang/SeqGSEA documentation built on Dec. 5, 2020, 5:52 p.m.