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MAMA (version 1.0.2)
Meta-Analysis of MicroArry
Description
Implementation of methods for microarray meta-analysis.
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Version
2.2.1
2.1.0
1.0.2
1.0.1
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Install
install.packages('MAMA')
Monthly Downloads
42
Version
1.0.2
License
GPL (>= 2)
Maintainer
Ivana Ihnatova
Last Published
October 1st, 2010
Functions in MAMA (1.0.2)
Search functions
gene.list
Intersect of gene lists
dataGEM
Data format converter
make.matrix
Function to make matrix for heatmap to compare results of several methods
gene.select.FC
Function to select genes according to fold change
compute.RQ
Function to compute R and Q statistics as defined in - see References
patternMatch
Function to count soft pattern matches
meta.test
Function to compute T-statistic and p-value in meta-analysis
fold.change
function to do compute fold change between two groups
MAPsig1
Pattern signifficance
ratio
Function to calculate the ratio of co-significant: expected/observed
patternMatch.strong
Function to count strong pattern matches
probs.to.matrix
Function to convert list to matrix
join.DEG
Function to join vectors of differentially expressed genes to one list
plotgene
Function to visuaze change in expression of one gene
sd.filter
Microarray probes filtering
mergedata
Function to do merge ExpressionSet objects
metaheat2
Function to do plot heatmap
MAP.HTMLanno
Function to do make annotation of vectors of probeset ID
rank.genes.adv
Function to rank genes
cv.filter
Microarray probes filtering
plotES
Function to do plots in combination of effect size method
MAPmatrix
Function to summarize binary matrix
join.results
Function to join results from meta-analysis to one list
metaheat
Display Data as Heatmap
entitybuild2
Function to calculate test statistic for microarray data
MAPsig2
Pattern signifficance
plotQvsChi
Function to plot quantiles of Cochran's Q statistic and Chi-square quantiles.
MAP.genes
Function to do assign probesets IDs to patterns
patternmatrix
Function to split binary vectors to matrix.
plotpattern
Function to do plot signifficance of Meta-Analysis Patterns
T.select
Function to help with selection of threshold for T-statistics
dataZ
Data format converter
conting.tab
Contingency table from gene lists
metalist.to.matrix
Function to do convert list to matrix
rank.genes
Rank genes
MCtest
Monte Carlo permutation test
dataSOGL
Data format converter
plotclinical
Plot of clinical variables
metagene
Function to do extract row from list of data.frames
patternToString
Function to convert rows of a matrix to strings
test.group.shuffle
Function to do compute test statistic iterativelly
Z
Function to compute Z-statistics in contingency table