addGenesToGoReport {MineICA} | R Documentation

## Add Symbol IDs to hyperGTest results

### Description

Add gene Symbols contained in gene sets selected as significant by `hyperGTest` function

### Usage

      addGenesToGoReport(hgOver, universe,
        db = c("GO", "KEGG"), onto = c("CC", "MF", "BP"),
        annotation = NULL, entrez2symbol = NULL)

### Arguments

`hgOver` | Output of function `hyperGTest`
`universe` | A vector including all IDs on which enrichment analysis was applied
`db` | The database to use, default is c("GO","KEGG")
`onto` | A string specifying the GO ontology to use. Must be one of "BP", "CC", or "MF", see `GOHyperGParams`. Only used when argument `db` is "GO".
`annotation` | An annotation package
`entrez2symbol` | A vector indexed by Entrez Gene ID and filled with the corresponding Gene Symbols

### Details

This function takes as inputs the outputs of `hyperGTest` which takes Entrez Gene IDs as inputs to perform the enrichment analysis. The goal of this function is to select the Entrez Gene IDs responsible for the significant enrichment of a given gene set and annotate them in to gene Symbol IDs. When the annotation package `annotation` was used to map feature IDs to Entrez Gene ID, it can also be used here to map Entrez and Symbol IDs. If the annotation package was not used, but the Entrez Gene IDs were directly provided to the hyperGtest function, `annotation` is expected to be NULL and `entrez2symbol` must be specified.

This function returns the outputs of function `hyperGTest` which contain:

DB, ID, Term

  The database, the gene set ID, and the gene Set name,

P-value

  probability of observing the number of genes annotated for the gene set among the selected gene list, knowing the total number of annotated genes among the universe

,

Expected counts

  expected number of genes in the selected gene list to be found at each tested category term/gene set,

Odds ratio

  odds ratio for each category term tested which is an indicator of the level of enrichment of genes within the list as against the universe,

Counts

  number of genes in the selected gene list which are annotated for the gene set,

Size

  number of genes from the universe annotated for the gene set.

### Value

A data.frame containing the summary of the output of function hyperGTest (`summary(hgOver)`) with an additional column providing the gene Symbols included in the significant gene sets.

### Author(s)

Anne Biton

### See Also

`hyperGTest`, `GOHyperGParams`

[Package MineICA version 1.27.0 Index]