Meta-Analysis of MicroArry


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Documentation for package ‘MAMA’ version 1.0.2

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compute.RQ Function to compute R and Q statistics as defined in - see References
conting.tab Contingency table from gene lists
cv.filter Microarray probes filtering
dataGEM Data format converter
dataSOGL Data format converter
dataZ Data format converter
entitybuild2 Function to calculate test statistic for microarray data
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
MAP.genes Function to do assign probesets IDs to patterns
MAP.HTMLanno Function to do make annotation of vectors of probeset ID
MAPmatrix Function to summarize binary matrix
MAPsig1 Pattern signifficance
MAPsig2 Pattern signifficance
MCtest Monte Carlo permutation test
mergedata Function to do merge ExpressionSet objects
meta.test Function to compute T-statistic and p-value in meta-analysis
metagene Function to do extract row from list of data.frames
metaheat Display Data as Heatmap
metaheat2 Function to do 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
patternmatrix Function to split binary vectors to matrix.
patternToString Function to convert rows of a matrix to strings
plotclinical Plot of clinical variables
plotES Function to do plots in combination of effect size method
plotgene 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.
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
T.select Function to help with selection of threshold for T-statistics
test.group.shuffle Function to do compute test statistic iterativelly
Z Function to compute Z-statistics in contingency table