# Meta-Analysis of MicroArray

## Documentation for package ‘MAMA’ version 2.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

as.list-method | Class "MetaArray" ~~~
clinical | Functions to retrieve and assign
clinical.sum | Function to calculate summaries of clinical data
clinical<- | Functions to retrieve and assign
clinical<--method | Functions to retrieve and assign
clinical<--method | Replacement Methods for 'MetaArray' object
clinical<--methods | Replacement Methods for 'MetaArray' object
colIntersect | Function to find intersect in columns of a data.frame
ColonData | Example dataset for meta-analysis of microarray
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
datanames | Functions to retrieve and assign
datanames<- | Functions to retrieve and assign
datanames<--method | Functions to retrieve and assign
datanames<--method | Replacement Methods for 'MetaArray' object
datanames<--methods | Replacement Methods for 'MetaArray' object
entitybuild2 | Function to calculate test statistic for microarray data
ES.GeneMeta | Wrapper function for combining the effect size as implemented in GeneMeta package
ES.GeneMeta.res | Wrapper function for combining the effect size as implemented in GeneMeta package
flip | Function to flip data frames
fold.change | Function to do compute fold change between two groups
GEDM | Functions to retrieve and assign
GEDM<- | Functions to retrieve and assign
GEDM<--method | Functions to retrieve and assign
GEDM<--method | Replacement Methods for 'MetaArray' object
GEDM<--methods | Replacement Methods for 'MetaArray' object
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
MAP.genes | Function to do assign probesets IDs to patterns
MAP.Matches | Wrapper function for MAP-Matches method
MAP.Matches.res | Wrapper function for MAP-Matches method
MAPmatrix | Function to summarize binary matrix
MAPsig1 | Pattern signifficance
MAPsig2 | Pattern signifficance
MCtest | Monte Carlo permutation test
mergedata | Function to merge data from MetaArray object
mergeExprs2 | Function to merge ExpressionSet object
meta.test | Function to compute T-statistic and p-value in meta-analysis
MetaArray-class | Class "MetaArray" ~~~
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
metaMA | Wrapper function for effect size or p-value combination methods
metaMA.res | Wrapper function for effect size or p-value combination methods
METRADISC | Wrapper function for METRADISC method
METRADISC.res | Wrapper function for METRADISC method
multExpFDR | Function for Meta-analysis of gene expression data
patternMatch | Function to count soft pattern matches
patternMatch.strong | Function to count strong pattern matches
patternmatrix | Function to split binary vectors to matrix.
patternToString | Function to convert rows of a matrix to strings
performSOGL | Function to perform analysis using Similarity of Ordered Gene Lists
plot-method | Class "MetaArray" ~~~
plot.SOGLresult | Function to plot an object of class SOGLresult
plotES | Function to do plots in combination of effect size method
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
plotQvsChi | Function to plot quantiles of Cochran's Q statistic and Chi-square quantiles.
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
print-method | Class "MetaArray" ~~~
probs.to.matrix | Function to convert list to matrix
RandomScore | Function to do compute random and subsampled similarity score
rank.genes | Rank genes
rank.genes.adv | Function to rank genes
RankProduct | Wrapper function for RankProduct method
RankProduct.res | Wrapper function for RankProduct method
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
show-method | Class "MetaArray" ~~~
sigScore | Function to calculate signifficance of similarity score
T.select | Function to help with selection of threshold for T-statistics
test.group.shuffle | Function to do compute test statistic iterativelly
VennMapper | Wrapper function for VennMapping
VennMapper.res | Wrapper function for VennMapping
Z | Function to compute Z-statistics in contingency table
zScoreFDR | Function for Meta-analysis of gene expression data
zScorePermuted | Function for Meta-analysis of gene expression data
zScores | Function for Meta-analysis of gene expression data