GOstats-package {GOstats} | R Documentation

## Tools for manipulating GO and microarrays.

### Description

A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.

### Details

Package: | GOstats
Version: | 1.7.4
Date: | 23-08-2006
biocViews: | Statistics, Annotation, GO, MultipleComparisons
Depends: | graph (>= 1.9.25), GO, annotate, RBGL, xtable, Biobase, genefilter, multtest, Category (>= 1.3.7), methods
Imports: | methods, Category
Suggests: | hgu95av2 (>= 1.6.0)
License: | Artistic

Index:

    ALL                     Acute Lymphoblastic Leukemia Data from the Ritz
                            Laboratory
    GOLeaves                Identify the leaves in a GO Graph
    GOstats-defunct         Defunct Functions in GOstats Package
    Ndists                  Distance matrices for the BCR/ABL and NEG
                            subgroups.
    compCorrGraph           A function to compute a correlation based graph
                            from Gene Expression Data
    compGdist               A function to compute the distance between
                            pairs of nodes in a graph.
    dropECode               Drop GO labels for specified Evidence Codes
    getEvidence             Get the Evidence codes for a set of GO terms.
    getGOTerm               Functions to Access GO data.
    getOntology             Get GO terms for a specified ontology
    hasGOannote             Check for GO annotation
    hyperG2Affy             A List of Affymetrix IDs from GOIDs
    hyperGtable             Table from GOHyperG
    idx2dimnames            Index to Dimnames
    makeGOGraph             Construct a GO Graph
    notConn                 Find genes that are not connected to the
                            others.
    oneGOGraph              Construct the GO graph given a set of leaves.
    shortestPath            Shortest Path Analysis
    simLL                   Functions to compute similarities between GO
                            graphs and also between LocusLink IDs based on
                            their induced GO graphs.
    triadCensus             Triad Functions

Further information is available in the following vignettes:

`GOstats` | Using GOstats (source, pdf)
`GOusage` | Basic GO Usage (source, pdf)
`GOvis` | Visualizing Data Using GOstats (source, pdf)

### Author(s)

R. Gentleman with contributions from S. Falcon

Maintainer: R. Gentleman <rgentlem@fhcrc.org>

[Package GOstats version 2.0.4 Index]