A wrapper function to implement the Hypergeometric test, HyperGTest found withing the Category and GOstats packages.

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Description

This function takes the instances of the hyperGParams and conducts a (conditional) test for over/under representation of some category under the Hypergeometric distribution.

Usage

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ppiHGTest4GO(parameter, filename, append=TRUE,
                      label = "Experiment name here",
                      typeGeneSet = "Describe the gene set here",
                      cs=50)

ppiHGTest4PFAM(parameter, filename, append = TRUE,
                           label = "Experiment Name Here",
                           typeGeneSet = "Describe the Gene Set Here",
                           cs = 50)

Arguments

parameter

An object of hyperGParams.

filename

A character vector. The name given to the .html file produced.

append

A logical. If multiple tests are conducted using the same filename, then the .html file will be appended if TRUE or over-written if FALSE.

label

A character. The should give a description of the experiment used to obtain the gene set.

typeGeneSet

A character: this character vector should adequately describe the gene set itself.

cs

A numeric. This gives a cut-off for the size of the categories in which we conduct the test.

Value

A instance of the class hyperGTest as well as an .html file.

Author(s)

T Chiang

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