ColonData               Example dataset for meta-analysis of microarray
ES.GeneMeta             Wrapper function for combining the effect size
                        as implemented in GeneMeta package
GEDM<--methods          Replacement Methods for 'MetaArray' object
MAP.Matches             Wrapper function for MAP-Matches method
MAP.genes               Function to do assign probesets IDs to patterns
MAPmatrix               Function to summarize binary matrix
MAPsig1                 Pattern signifficance
MAPsig2                 Pattern signifficance
MCtest                  Monte Carlo permutation test
METRADISC               Wrapper function for METRADISC method
MetaArray-class         Class "MetaArray" ~~~
RandomScore             Function to do compute random and subsampled
                        similarity score
RankProduct             Wrapper function for RankProduct method
T.select                Function to help with selection of threshold
                        for T-statistics
VennMapper              Wrapper function for VennMapping
Z                       Function to compute Z-statistics in contingency
                        table
clinical                Functions to retrieve and assign
clinical.sum            Function to calculate summaries of clinical
                        data
colIntersect            Function to find intersect in columns of a
                        data.frame
commonGenes             Function to compute number of common genes in
                        ordered gene lists
compute.RQ              Function to compute R and Q statistics as
                        defined in - see References
computeAlpha            Function to do compute tunning parameter alpha
computeOrdering         Function to compute ordered gene lists
conting.tab             Contingency table from gene lists
cv.filter               Microarray probes filtering
entitybuild2            Function to calculate test statistic for
                        microarray data
flip                    Function to flip data frames
fold.change             Function to do compute fold change between two
                        groups
gene.list               Intersect of gene lists
gene.select.FC          Function to select genes according to fold
                        change
join.DEG                Function to join vectors of differentially
                        expressed genes to one list
join.results            Function to join results from meta-analysis to
                        one list
make.matrix             Function to make matrix for heatmap to compare
                        results of several methods
mergeExprs2             Function to merge ExpressionSet object
mergedata               Function to merge data from MetaArray object
meta.test               Function to compute T-statistic and p-value in
                        meta-analysis
metaMA                  Wrapper function for effect size or p-value
                        combination methods
metagene                Function to do extract row from list of
                        data.frames
metaheat                Display Data as Heatmap
metaheat2               Function to plot heatmap
metalist.to.matrix      Function to do convert list to matrix
patternMatch            Function to count soft pattern matches
patternMatch.strong     Function to count strong pattern matches
patternToString         Function to convert rows of a matrix to strings
patternmatrix           Function to split binary vectors to matrix.
performSOGL             Function to perform analysis using Similarity
                        of Ordered Gene Lists
plot.SOGLresult         Function to plot an object of class SOGLresult
plotES                  Function to do plots in combination of effect
                        size method
plotQvsChi              Function to plot quantiles of Cochran's Q
                        statistic and Chi-square quantiles.
plotgene                Function to visuaze change in expression of one
                        gene
plotgene2               Function to visuaze change in expression of one
                        gene
plotpattern             Function to do plot signifficance of
                        Meta-Analysis Patterns
posterior.mean          Function to calculate posterior mean
                        differential expression
prelimScore             Function compute preliminary Similarity Score
                        for Ordered Gene Lists
prepareData             Function to prepare data
preparePermutations     Function to prepare permutation and subsamples
probs.to.matrix         Function to convert list to matrix
rank.genes              Rank genes
rank.genes.adv          Function to rank genes
ratio                   Function to calculate the ratio of
                        co-significant: expected/observed
sd.filter               Microarray probes filtering
selectAlpha             Function to select the most optimal alpha
                        parameter
selectClass             Function to select class labels from MetaArray
                        object
selectGenes             Function to select genes that account for
                        Similarity score
sigScore                Function to calculate signifficance of
                        similarity score
test.group.shuffle      Function to do compute test statistic
                        iterativelly
zScores                 Function for Meta-analysis of gene expression
                        data
