Atong                   Systematic genetic analysis with ordered arrays
                        of yeast deletion Tong et. al. (2004).
AtongFnDomain           The functional domains shared by the tested
                        pairs in Tong et al experiment.
AtongPair               Data frame the pair of yeast gene tested in
                        Tong et al. 2004.
Boeke2006raw            Incidence matrix of Synthetic Lethal
                        interaction from the Boeke Lab
SDL                     The Association matrix for the synthetic dosage
                        lethal screens in Yeast.
SGA                     Systematic genetic analysis with ordered arrays
                        of yeast deletion.
SGD.SL                  Interaction data from the Saccharomyces Genome
                        Database
TFmat                   Transcription Factor Binding Affinities
byComplex               Evaluate protein co-membership within cellular
                        organizational units
comemberIn              Retrieve the biological complexes.
compare                 Compare observed data to expected in
                        permutation models
congruence              Calculate congruence score between pairs of of
                        genes sharing pattern of synthetic genetic
                        interactions (Ye et al. (2005)).
createSquareMatrix      Create a square matrix
dSLAM.GPL1444           dSLAM platform used for Synthetic Lethal
                        screens in the Boeke Lab
domainDist              Finds the number of gene sets for each shared
                        domain
essglist                The list of yeast essential genes
getInteraction          Count genetic interactions within and between
                        cellular organizational units
getSharedDomains        Find domains shared by a given list of gene
                        names.
getSharedInteraction    Calculate the number of shared synthetic
                        genetic interactions between pairs of genes.
getTestedPairs          Find interacting and non-interacting tested
                        pairs from an genetic interaction matrix.
getUniquePairs          Find unique pairs from an genetic interaction
                        matrix.
gi2005                  Genetic Interaction Data (EMAP) from the yeast
                        early secretory pathway
gi2007                  Synthetic Genetic Interaction data from Collins
                        et al
gi2Interactome          Reduce genetic interactions matrix
hyperG                  Hypergeometric test
iSummary                Summarize cellular organizational units sharing
                        genetic interaction
modelSLGI               Permutation model for assessing synthetic
                        genetic interactions in cellular organizational
                        units.
normInteraction         Normalize a matrix of biological interactions
plot                    Graphical method to represent the result of the
                        modelSLGI .
seqMatcherAlign         Functions to do local alignment of two
                        sequences using EMBOSS matcher
sharedBy                Find the gene pairs that share a domain.
sharedInt               List shared genetic interactions between genes
siResult-class          A class for representing the result of the SLGI
                        graph permutation model.
test2Interact           Summarize genetic interactions within or
                        between cellular organizational units
topInteraction          Extract interacting biological complexes
twoWayTable             Generate two-way table for genetic interaction
                        data
withinComplex           Search for protein co-membership within
                        complexes.
