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MAMA (version 2.1.0)
Meta-Analysis of MicroArry
Description
Implementation of methods for microarray meta-analysis.
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Install
install.packages('MAMA')
Monthly Downloads
42
Version
2.1.0
License
GPL (>= 2)
Maintainer
Ivana Ihnatova
Last Published
September 17th, 2012
Functions in MAMA (2.1.0)
Search functions
MAPsig2
Pattern signifficance
colIntersect
Function to find intersect in columns of a data.frame
clinical.sum
Function to calculate summaries of clinical data
metagene
Function to do extract row from list of data.frames
sd.filter
Microarray probes filtering
selectGenes
Function to select genes that account for Similarity score
fold.change
Function to do compute fold change between two groups
plotgene2
Function to visuaze change in expression of one gene
metalist.to.matrix
Function to do convert list to matrix
sigScore
Function to calculate signifficance of similarity score
METRADISC
Wrapper function for METRADISC method
RandomScore
Function to do compute random and subsampled similarity score
rank.genes
Rank genes
join.results
Function to join results from meta-analysis to one list
patternToString
Function to convert rows of a matrix to strings
conting.tab
Contingency table from gene lists
gene.select.FC
Function to select genes according to fold change
prelimScore
Function compute preliminary Similarity Score for Ordered Gene Lists
plotpattern
Function to do plot signifficance of Meta-Analysis Patterns
MAPsig1
Pattern signifficance
patternMatch
Function to count soft pattern matches
probs.to.matrix
Function to convert list to matrix
Z
Function to compute Z-statistics in contingency table
commonGenes
Function to compute number of common genes in ordered gene lists
gene.list
Intersect of gene lists
metaheat
Display Data as Heatmap
plotQvsChi
Function to plot quantiles of Cochran's Q statistic and Chi-square quantiles.
performSOGL
Function to perform analysis using Similarity of Ordered Gene Lists
metaMA
Wrapper function for effect size or p-value combination methods
rank.genes.adv
Function to rank genes
entitybuild2
Function to calculate test statistic for microarray data
plotES
Function to do plots in combination of effect size method
zScores
Function for Meta-analysis of gene expression data
ES.GeneMeta
Wrapper function for combining the effect size as implemented in GeneMeta package
metaheat2
Function to plot heatmap
MAP.Matches
Wrapper function for MAP-Matches method
TSP
Wrapper function for top-scoring pair
MCtest
Monte Carlo permutation test
join.DEG
Function to join vectors of differentially expressed genes to one list
patternmatrix
Function to split binary vectors to matrix.
ratio
Function to calculate the ratio of co-significant: expected/observed
preparePermutations
Function to prepare permutation and subsamples
plot.SOGLresult
Function to plot an object of class SOGLresult
selectClass
Function to select class labels from MetaArray object
compute.RQ
Function to compute R and Q statistics as defined in - see References
ColonData
Example dataset for meta-analysis of microarray
VennMapper
Wrapper function for VennMapping
computeAlpha
Function to do compute tunning parameter alpha
meta.test
Function to compute T-statistic and p-value in meta-analysis
make.matrix
Function to make matrix for heatmap to compare results of several methods
MetaArray-class
Class "MetaArray" ~~~
flip
Function to flip data frames
prepareData
Function to prepare data
MAPmatrix
Function to summarize binary matrix
selectAlpha
Function to select the most optimal alpha parameter
mergedata
Function to merge data from MetaArray object
T.select
Function to help with selection of threshold for T-statistics
cv.filter
Microarray probes filtering
computeOrdering
Function to compute ordered gene lists
test.group.shuffle
Function to do compute test statistic iterativelly
MAP.genes
Function to do assign probesets IDs to patterns
RankProduct
Wrapper function for RankProduct method
patternMatch.strong
Function to count strong pattern matches