hgTests {ppiStats} | R Documentation

## 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.

### Author(s)

T Chiang

[Package ppiStats version 1.53.1 Index]