Description Usage Arguments Value Note Author(s) References See Also Examples

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.

1 | ```
DENBStat4GSEA(cds)
``` |

`cds` |
A CountDataSet 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`

1 2 3 4 5 6 | ```
data(RCS_example, package="SeqGSEA")
geneCounts <- getGeneCount(RCS_example)
label <- label(RCS_example)
DEG <- runDESeq(geneCounts, label)
DEGres <- DENBStat4GSEA(DEG)
head(DEGres)
``` |

SeqGSEA documentation built on May 31, 2017, 3:19 p.m.

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