addGenesToGoReport: Add Symbol IDs to hyperGTest results
In MineICA: Analysis of an ICA decomposition obtained on genomics data

Description Usage Arguments Details Value Author(s) See Also

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

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

`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

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.

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.

Anne Biton

hyperGTest, GOHyperGParams

MineICA documentation built on Nov. 8, 2020, 5:35 p.m.