\HeaderA{GOstats-package}{Tools for manipulating GO and microarrays.}{GOstats.Rdash.package}
\aliasA{GOstats}{GOstats-package}{GOstats}
\keyword{package}{GOstats-package}
\begin{Description}\relax
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.
\end{Description}
\begin{Details}\relax
\Tabular{ll}{
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:
\begin{alltt}
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 Entrez Gene IDs based on
                        their induced GO graphs.
triadCensus             Triad Functions
\end{alltt}

Further information is available in the following vignettes:
\Tabular{ll}{
\code{GOstats} & Using GOstats (source, pdf)\\
\code{GOusage} & Basic GO Usage (source, pdf)\\
\code{GOvis} & Visualizing Data Using GOstats (source, pdf)\\
}
\end{Details}
\begin{Author}\relax
R. Gentleman with contributions from S. Falcon

Maintainer: R. Gentleman <rgentlem@fhcrc.org>
\end{Author}

