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MAMA (version 2.2.1)

Meta-Analysis of MicroArray

Description

Implementation of methods for microarray meta-analysis.

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Version

Install

install.packages('MAMA')

Monthly Downloads

35

Version

2.2.1

License

GPL (>= 2)

Maintainer

Ivana Ihnatova

Last Published

April 30th, 2013

Functions in MAMA (2.2.1)

Z

Function to compute Z-statistics in contingency table
RandomScore

Function to do compute random and subsampled similarity score
clinical.sum

Function to calculate summaries of clinical data
MCtest

Monte Carlo permutation test
MAPsig1

Pattern signifficance
computeOrdering

Function to compute ordered gene lists
entitybuild2

Function to calculate test statistic for microarray data
mergedata

Function to merge data from MetaArray object
RankProduct

Wrapper function for RankProduct method
computeAlpha

Function to do compute tunning parameter alpha
ColonData

Example dataset for meta-analysis of microarray
MetaArray-class

Class "MetaArray" ~~~
T.select

Function to help with selection of threshold for T-statistics
join.results

Function to join results from meta-analysis to one list
rank.genes

Rank genes
MAP.genes

Function to do assign probesets IDs to patterns
plotgene2

Function to visuaze change in expression of one gene
VennMapper

Wrapper function for VennMapping
test.group.shuffle

Function to do compute test statistic iterativelly
prelimScore

Function compute preliminary Similarity Score for Ordered Gene Lists
metaheat2

Function to plot heatmap
selectAlpha

Function to select the most optimal alpha parameter
metalist.to.matrix

Function to do convert list to matrix
MAP.Matches

Wrapper function for MAP-Matches method
clinical

Functions to retrieve and assign
flip

Function to flip data frames
colIntersect

Function to find intersect in columns of a data.frame
selectGenes

Function to select genes that account for Similarity score
rank.genes.adv

Function to rank genes
gene.select.FC

Function to select genes according to fold change
ratio

Function to calculate the ratio of co-significant: expected/observed
GEDM<--methods

Replacement Methods for MetaArray object
patternToString

Function to convert rows of a matrix to strings
plotpattern

Function to do plot signifficance of Meta-Analysis Patterns
metaheat

Display Data as Heatmap
probs.to.matrix

Function to convert list to matrix
performSOGL

Function to perform analysis using Similarity of Ordered Gene Lists
sd.filter

Microarray probes filtering
commonGenes

Function to compute number of common genes in ordered gene lists
patternmatrix

Function to split binary vectors to matrix.
plot.SOGLresult

Function to plot an object of class SOGLresult
fold.change

Function to do compute fold change between two groups
MAPmatrix

Function to summarize binary matrix
ES.GeneMeta

Wrapper function for combining the effect size as implemented in GeneMeta package
METRADISC

Wrapper function for METRADISC method
gene.list

Intersect of gene lists
compute.RQ

Function to compute R and Q statistics as defined in - see References
sigScore

Function to calculate signifficance of similarity score
patternMatch

Function to count soft pattern matches
cv.filter

Microarray probes filtering
make.matrix

Function to make matrix for heatmap to compare results of several methods
plotgene

Function to visuaze change in expression of one gene
patternMatch.strong

Function to count strong pattern matches
plotQvsChi

Function to plot quantiles of Cochran's Q statistic and Chi-square quantiles.
selectClass

Function to select class labels from MetaArray object
zScores

Function for Meta-analysis of gene expression data
conting.tab

Contingency table from gene lists
preparePermutations

Function to prepare permutation and subsamples
join.DEG

Function to join vectors of differentially expressed genes to one list
metaMA

Wrapper function for effect size or p-value combination methods
meta.test

Function to compute T-statistic and p-value in meta-analysis
metagene

Function to do extract row from list of data.frames
MAPsig2

Pattern signifficance
prepareData

Function to prepare data
plotES

Function to do plots in combination of effect size method