hyperGGeneric: Perform a hypergeometric test as in a Gene Ontology analysis...

In jotsetung/unsoRted: Unsorted R functions and utilities

Description

This function performs a hypergeometric test, as performed by the “Category” package for a Gene Ontology analysis, on any user-defined and provided categories.

Usage

hyperGGeneric( fg.gns=character(), bg.gns=character(), x, proc="BH" )

Arguments

fg.gns	A character vector of e.g. gene ids that should be tested for significant over-representation in the categories provided by the argument “x”.
bg.gns	A character vector defining the background genes (or gene universe as called in the “Category” package). Should be e.g. all genes detected on the microarray and used in the test to define the “fg.gns”.
x	A list defining the categories. This should be a list of character vectors, the names of the list specifying the category names and the values the genes associated with the category.
method	The method to be used for multiple hypothesis testing. Allowed are all values of p.adjust.methods.

Value

A data.frame with columns:

“Term”	The category name
“Pvalue”	The (raw) p-value from the hypergeometric test.
“padj”	The adjusted p-value, according to the specified method.
“Count”	The number of “fg.gns” associated with the category.
“Size”	The total number of “bg.gns” associated with the category.
“perc”	The percentage of “fg.gns” associated with the category (related to the number of “bg.gns” in the category).
“Fold.Enr”	The ratio between the proportion of genes in the category being significantly regulated (i.e. Count/Size) against the proportion of regulated genes relative to the total amount of detected and tested genes (i.e. the ratio between the fg.gns/bg.gns).
“fg.gns”	The list of all “fg.gns” associated to the category (as a string, with elements separated by a “;”).
“bg.gns”	The list of all “bg.gns” associated to the category (as a string, with elements separated by a “;”).

Author(s)

Daniel Bindreither, Johannes Rainer

References

http://bioinfo.i-med.ac.at

jotsetung/unsoRted documentation built on May 19, 2019, 9:42 p.m.