pValue-method: ~~ Methods for Function 'pValue' ~~

In cpvSNP: Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

Description

This function returns the calculated p-value for a specified GeneSet or a list of p-values for a GeneSetCollection.

Usage

pValue(object)

Arguments

object

An object of type GeneSetResult, VEGASResult, GLOSSIResult, GeneSetResultCollection, VEGASResultCollection, or GLOSSIResultCollection

Methods

Defined methods include:

signature(object = "VEGASResult")

Returns the calculated p-value for a specified VEGASResult object

signature(object = "GeneSetResult")

Returns the calculated p-value for a specified GeneSetResult object

signature(object = "GLOSSIResult")

Returns the calculated p-value for a specified GLOSSIResult object

signature(object = "VEGASResultCollection")

Returns a list of calculated p-values for a VEGASResultCollection object (1 for each set)

signature(object = "GeneSetResultCollection")

Returns a list of calculated p-values for a GeneSetResultCollection object (1 for each set)

signature(object = "GLOSSIResultCollection")

Returns a list of calculated p-values for a GLOSSIResultCollection object (1 for each set)

Value

Returns a decimal p-value corresponding to the gene set or a list of p-values corresponding to the gene set collection.

Author(s)

Caitlin McHugh

See Also

VEGASResult-class, geneSetName

Examples

	## Not run: 
	pValue( vegas(geneSet, assoc_table, ldMatrix) ) 
	
## End(Not run)

cpvSNP documentation built on Nov. 8, 2020, 6 p.m.