Meta-Analysis of MicroArray


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Documentation for package ‘MAMA’ version 2.2.1

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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