addGenesToGoReport: Add Symbol IDs to hyperGTest results

In bitona/MineICA: Analysis of an ICA decomposition obtained on genomics data

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

bitona/MineICA documentation built on April 23, 2023, 1:41 p.m.