SeqGeneSet-class {SeqGSEA} | R Documentation

## Class `"SeqGeneSet"`

### Description

SeqGeneSet class

### Objects from the Class

Objects can be created by calls of the function `newGeneSets`.

### Slots

`name`:

  Object of class `"character"` the name of this gene set category

`sourceFile`:

  Object of class `"character"` the source file of gene set category

`geneList`:

  Object of class `"character"` the gene ID list indicating genes involved in this GSEA

`GS`:

  Object of class `"list"` a list of gene indexes corresponding to `geneList`, each element in the list indicating which genes are in each gene set of this SeqGeneSet object

`GSNames`:

  Object of class `"character"`. Gene set names.

`GSDescs`:

  Object of class `"character"`. Gene set descriptions.

`GSSize`:

  Object of class `"numeric"`. Gene set sizes.

`GSSizeMin`:

  Object of class `"numeric"`. The minimum gene set size to be analyzed.

`GSSizeMax`:

  Object of class `"numeric"`. The maximum gene set size to be analyzed.

`GS.Excluded`:

  Object of class `"list"`. Gene sets excluded to be analyzed.

`GSNames.Excluded`:

  Object of class `"character"`. Gene set names excluded to be analyzed.

`GSDescs.Excluded`:

  Object of class `"character"`. Gene set descriptions excluded to be analyzed.

`GSEA.ES`:

  Object of class `"numeric"`. Enrichment scores.

`GSEA.ES.pos`:

  Object of class `"numeric"`. The positions where enrichment scores appear.

`GSEA.ES.perm`:

  Object of class `"matrix"`. The enrichment scores of the permutation data sets.

`GSEA.score.cumsum`:

  Object of class `"matrix"`. Running enrichment scores.

`GSEA.normFlag`:

  Object of class `"logical"`. Logical indicating whether `GSEA.ES` has been normalized.

`GSEA.pval`:

  Object of class `"numeric"`. P-values of each gene set.

`GSEA.FWER`:

  Object of class `"numeric"`. Family-wise error rate of each gene set.

`GSEA.FDR`:

  Object of class `"numeric"`. False discovery rate of each gene set.

`sc.ES`:

  Object of class `"numeric"`. Enrichment scores in scGSEA.

`sc.ES.perm`:

  Object of class `"matrix"`. The enrichment scores of the permutation data sets in scGSEA.

`sc.normFlag`:

  Object of class `"logical"`. Logical indicating whether `sc.ES` has been normalized in scGSEA.

`scGSEA`:

  Object of class `"logical"`. Whether or not used for scGSEA.

`sc.pval`:

  Object of class `"numeric"`. P-values of each gene set in scGSEA.

`sc.FWER`:

  Object of class `"numeric"`. Family-wise error rate of each gene set in scGSEA.

`sc.FDR`:

  Object of class `"numeric"`. False discovery rate of each gene set in scGSEA.

`version`:

  Object of class `"Versions"`. Version information.

### Methods

[

  Get a sub-list of gene sets, and return a SeqGeneSet object.

show

  Show basic information of the SeqGeneSet object.

### Author(s)

Xi Wang, xi.wang@newcastle.edu.au

### 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

`newGeneSets`, `size`, `geneSetNames`, `geneSetDescs`, `geneSetSize`

### Examples

    showClass("SeqGeneSet")

[Package SeqGSEA version 1.27.0 Index]