Add gene Symbols contained in gene sets selected as
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Output of function
A vector including all IDs on which enrichment analysis was applied
The database to use, default is c("GO","KEGG")
A string specifying the GO ontology to use.
Must be one of "BP", "CC", or "MF", see
An annotation package
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,
expected to be NULL and
entrez2symbol must be
This function returns the outputs of function
hyperGTest which contain:
The database, the gene set ID, and the gene Set name,
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 number of genes in the selected gene list to be found at each tested category term/gene set,
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,
number of genes in the selected gene list which are annotated for the gene set,
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.
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