DENBStat4GSEA {SeqGSEA} | R Documentation |
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.
DENBStat4GSEA(dds)
dds |
A DESeqDataSet object with size factors and dispersion parameters estimated. Recommended to take the output of |
A data frame containing each gene's expression means and variances in each group, and each gene's DE NB-statistics.
The results with the output of DENBStatPermut4GSEA
can also be used to run DEpermutePval
.
Xi Wang, xi.wang@newcastle.edu.au
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.
DENBTest
,
runDESeq
,
DENBStatPermut4GSEA
data(RCS_example, package="SeqGSEA") geneCounts <- getGeneCount(RCS_example) label <- label(RCS_example) DEG <- runDESeq(geneCounts, label) DEGres <- DENBStat4GSEA(DEG) head(DEGres)