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MAMA (version 1.0.1)
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
1.0.1
License
GPL (>= 2)
Maintainer
Ivana Ihnatova
Last Published
May 26th, 2010
Functions in MAMA (1.0.1)
Search functions
test.group.shuffle
Function to do compute test statistic iterativelly
dataGEM
Data format converter
MAP.HTMLanno
Function to do make annotation of vectors of probeset ID
patternmatrix
Function to split binary vectors to matrix.
sd.filter
Microarray probes filtering
cv.filter
Microarray probes filtering
plotgene
Function to plot various characteristics of gene expression
ratio
Function to calculate the ratio of co-significant: expected/observed
plotclinical
Plot of clinical variables
Z
Function to compute Z-statistics in contingency table
patternMatch.strong
Function to count strong pattern matches
gene.select.FC
Function to select genes according to fold change
dataSOGL
Data format converter
MAP.genes
Function to do assign probesets IDs to patterns
patternToString
Function to convert rows of a matrix to strings
MAPsig1
Pattern signifficance
dataZ
Data format converter
compute.RQ
Function to compute R and Q statistics as defined in - see References
MCtest
Monte Carlo permutation test
rank.genes
Rank genes
make.matrix
Function to make matrix for heatmap to compare results of several methods
entitybuild2
Function to calculate test statistic for microarray data
fold.change
function to do compute fold change between two groups
metagene
Function to do extract row from list of data.frames
gene.list
Intersect of gene lists
MAPsig2
Pattern signifficance
conting.tab
Contingency table from gene lists
metalist.to.matrix
Function to do convert list to matrix
metaheat2
Function to do plot heatmap
metaheat
Display Data as Heatmap
probs.to.matrix
Function to convert list to matrix
patternMatch
Function to count soft pattern matches