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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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Version

Install

install.packages('MAMA')

Monthly Downloads

8

Version

2.1.0

License

GPL (>= 2)

Maintainer

Ivana Ihnatova

Last Published

September 17th, 2012

Functions in MAMA (2.1.0)

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