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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

Install

install.packages('MAMA')

Monthly Downloads

22

Version

1.0.2

License

GPL (>= 2)

Maintainer

Ivana Ihnatova

Last Published

October 1st, 2010

Functions in MAMA (1.0.2)

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