fisher_score-methods: Hypergeometric probability of gene set enrichment
In gCMAP: Tools for Connectivity Map-like analyses

Description Arguments Value Methods Note See Also Examples

A method for computing enrichment probilities based on the hypergeometric distribution. This method performs an over-representation analysis by generating 2x2 incidence matrices for gene sets provided as 'query' and 'sets' as GeneSet, SignedGeneSet, GeneSetCollection or CMAPCollection objects. If 'sets' is an NChannelSet object with quantitative data, gene sets are induced on the fly from the channel specified by the 'element' parameter.

`query`	A `CMAPCollection`, `GeneSet`, or `GeneSetCollection` object containing the 'query' gene sets to compare against the 'sets'
`sets`	A `CMAPCollection`, `GeneSetCollection` or `GeneSet` object
`universe`	A character string of gene ids for all genes that could potentially be of interest, e.g. all genes represented on a microarray, all annotated genes, etc.
`keep.scores`	Logical: store the identifiers for the genes detected in 'query' and 'sets' ? (Default: FALSE) The size of the generated CMAPResults object increases with the number of contained gene sets. For very large collections, setting this parameter to 'TRUE' may require large amounts of memory.
`element`	A character string corresponding to the assayDataElementName of the NChannelSet object to be thresholded on the fly with the `induceCMAPCollection`.
`lower`	The lower threshold for the `induceCMAPCollection`.
`higher`	The 'higher' threshold for the `induceCMAPCollection`.
`min.set.size`	Number of genes a gene set induced by `induceCMAPCollection` needs to contain to be included in the analysis (Default:5).
`...`	Additional arguments passed to downstream methods.

A CMAPResults object

signature(query = "CMAPCollection", sets = "CMAPCollection", universe = "character")
signature(query = "CMAPCollection", sets = "NChannelSet", universe = "character")
signature(query = "SignedGeneSet", sets = "CMAPCollection", universe = "character")
signature(query = "SignedGeneSet", sets = "NChannelSet", universe = "character")
signature(query = "GeneSet", sets = "CMAPCollection", universe = "character")
signature(query = "GeneSet", sets = "NChannelSet", universe = "character")
signature(query = "GeneSetCollection", sets = "CMAPCollection", universe = "character")
signature(query = "GeneSetCollection", sets = "NChannelSet", universe = "character")
signature(query = "GeneSet", sets = "GeneSetCollection", universe = "character")
signature(query = "CMAPCollection", sets = "GeneSetCollection", universe = "character")
signature(query = "GeneSetCollection", sets = "GeneSetCollection", universe = "character")
signature(query = "GeneSet", sets = "GeneSet", universe = "character")

p-values are corrected for multiple testing separately for each query set, but not across multiple queries.

fisher.test

data(gCMAPData)

gene.set.collection <- induceCMAPCollection(gCMAPData, "z", higher=2, lower=-2)

## compare all gene sets in the gene.set.collection to each other
universe = featureNames(gCMAPData)
fisher_score(gene.set.collection, gene.set.collection, universe = universe)