ppiStats (version 1.38.0)

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

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

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.