MAMA: Meta-Analysis of MicroArray

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Implementation of methods for microarray meta-analysis.

Author
Ivana Ihnatova <184415@mail.muni.cz>.
Date of publication
2013-04-30 06:22:29
Maintainer
Ivana Ihnatova <184415@mail.muni.cz>
License
GPL (>= 2)
Version
2.2.1

View on CRAN

Man pages

clinical
Functions to retrieve and assign
clinical.sum
Function to calculate summaries of clinical data
colIntersect
Function to find intersect in columns of a data.frame
ColonData
Example dataset for meta-analysis of microarray
commonGenes
Function to compute number of common genes in ordered gene...
computeAlpha
Function to do compute tunning parameter alpha
computeOrdering
Function to compute ordered gene lists
compute.RQ
Function to compute R and Q statistics as defined in - see...
conting.tab
Contingency table from gene lists
cv.filter
Microarray probes filtering
entitybuild2
Function to calculate test statistic for microarray data
ES.GeneMeta
Wrapper function for combining the effect size as implemented...
flip
Function to flip data frames
fold.change
Function to do compute fold change between two groups
gene.list
Intersect of gene lists
gene.select.FC
Function to select genes according to fold change
join.DEG
Function to join vectors of differentially expressed genes to...
join.results
Function to join results from meta-analysis to one list
make.matrix
Function to make matrix for heatmap to compare results of...
MAP.genes
Function to do assign probesets IDs to patterns
MAP.Matches
Wrapper function for MAP-Matches method
MAPmatrix
Function to summarize binary matrix
MAPsig1
Pattern signifficance
MAPsig2
Pattern signifficance
MCtest
Monte Carlo permutation test
mergedata
Function to merge data from MetaArray object
MetaArray
Class "MetaArray" ~~~
metagene
Function to do extract row from list of data.frames
metaheat
Display Data as Heatmap
metaheat2
Function to plot heatmap
metalist.to.matrix
Function to do convert list to matrix
metaMA
Wrapper function for effect size or p-value combination...
meta.test
Function to compute T-statistic and p-value in meta-analysis
methods
Replacement Methods for 'MetaArray' object
METRADISC
Wrapper function for METRADISC method
patternMatch
Function to count soft pattern matches
patternMatch.strong
Function to count strong pattern matches
patternmatrix
Function to split binary vectors to matrix.
patternToString
Function to convert rows of a matrix to strings
performSOGL
Function to perform analysis using Similarity of Ordered Gene...
plotES
Function to do plots in combination of effect size method
plotgene
Function to visuaze change in expression of one gene
plotgene2
Function to visuaze change in expression of one gene
plotpattern
Function to do plot signifficance of Meta-Analysis Patterns
plotQvsChi
Function to plot quantiles of Cochran's Q statistic and...
plot.SOGLresult
Function to plot an object of class SOGLresult
prelimScore
Function compute preliminary Similarity Score for Ordered...
prepareData
Function to prepare data
preparePermutations
Function to prepare permutation and subsamples
probs.to.matrix
Function to convert list to matrix
RandomScore
Function to do compute random and subsampled similarity score
rank.genes
Rank genes
rank.genes.adv
Function to rank genes
RankProduct
Wrapper function for RankProduct method
ratio
Function to calculate the ratio of co-significant:...
sd.filter
Microarray probes filtering
selectAlpha
Function to select the most optimal alpha parameter
selectClass
Function to select class labels from MetaArray object
selectGenes
Function to select genes that account for Similarity score
sigScore
Function to calculate signifficance of similarity score
test.group.shuffle
Function to do compute test statistic iterativelly
T.select
Function to help with selection of threshold for T-statistics
VennMapper
Wrapper function for VennMapping
Z
Function to compute Z-statistics in contingency table
zScores
Function for Meta-analysis of gene expression data

Files in this package

MAMA
MAMA/MD5
MAMA/vignettes
MAMA/vignettes/upquote.sty
MAMA/vignettes/MAMA.rnw
MAMA/vignettes/inconsolata.sty
MAMA/vignettes/fancyvrb.sty
MAMA/Sweave
MAMA/Sweave/upquote.sty
MAMA/Sweave/Sweave.sty
MAMA/Sweave/MAMA_supershort.rnw
MAMA/Sweave/MAMA_supershort.pdf
MAMA/Sweave/MAMA_short.rnw
MAMA/Sweave/MAMA_full.toc
MAMA/Sweave/MAMA_full.tex
MAMA/Sweave/MAMA_full.synctex.gz
MAMA/Sweave/MAMA_full.rnw
MAMA/Sweave/MAMA_full.pdf
MAMA/Sweave/MAMA_full.log
MAMA/Sweave/MAMA_full.aux
MAMA/Sweave/MAMA_full-076.pdf
MAMA/Sweave/MAMA_full-075.pdf
MAMA/Sweave/MAMA_full-073.pdf
MAMA/Sweave/MAMA_full-072.pdf
MAMA/Sweave/MAMA_full-071.pdf
MAMA/Sweave/MAMA_full-070.pdf
MAMA/Sweave/MAMA_full-069.pdf
MAMA/Sweave/MAMA_full-068.pdf
MAMA/Sweave/MAMA_full-067.pdf
MAMA/Sweave/MAMA_full-061.pdf
MAMA/Sweave/MAMA_full-060.pdf
MAMA/Sweave/MAMA_full-056.pdf
MAMA/Sweave/MAMA_full-055.pdf
MAMA/Sweave/MAMA_full-054.pdf
MAMA/Sweave/MAMA_full-035.pdf
MAMA/Sweave/MAMA_full-034.pdf
MAMA/Sweave/MAMA_full-031.pdf
MAMA/Sweave/MAMA_full-022.pdf
MAMA/Sweave/MAMA_full-019.pdf
MAMA/Sweave/MAMA_full-018.pdf
MAMA/Sweave/MAMA_full-016.pdf
MAMA/Sweave/MAMA_full-015.pdf
MAMA/Sweave/MAMA_full-014.pdf
MAMA/Sweave/MAMA.toc
MAMA/Sweave/MAMA.tex
MAMA/Sweave/MAMA.synctex.gz
MAMA/Sweave/MAMA.pdf
MAMA/Sweave/MAMA.log
MAMA/Sweave/MAMA.aux
MAMA/Sweave/MAMA-026.pdf
MAMA/Sweave/MAMA-023.pdf
MAMA/Sweave/MAMA-021.pdf
MAMA/Sweave/MAMA-019.pdf
MAMA/Sweave/MAMA-018.pdf
MAMA/Sweave/MAMA-008.pdf
MAMA/Sweave/MAMA-007.pdf
MAMA/Sweave/MAMA-006.pdf
MAMA/Sweave/inconsolata.sty
MAMA/Sweave/fancyvrb.sty
MAMA/R
MAMA/R/zScores.R
MAMA/R/zScorePermuted.R
MAMA/R/zScoreFDR.R
MAMA/R/Z.R
MAMA/R/Wrappers.R
MAMA/R/VennMap.R
MAMA/R/T.select.R
MAMA/R/SOGL_final_new.R
MAMA/R/sd.filter.R
MAMA/R/ratio.R
MAMA/R/rank.genes.R
MAMA/R/rank.genes.adv.R
MAMA/R/probs.to.matrix.R
MAMA/R/plotgene2.R
MAMA/R/plotgene.r
MAMA/R/plot.SOGLresult.R
MAMA/R/plot.QvsChi.R
MAMA/R/plot.ES.R
MAMA/R/plot.clinical.R
MAMA/R/patternToString.R
MAMA/R/patternmatrix.R
MAMA/R/patternMatch.strong.R
MAMA/R/patternMatch.R
MAMA/R/multExpFDR.R
MAMA/R/METRADISC.R
MAMA/R/metalist.to.matrix.R
MAMA/R/metaheat2.R
MAMA/R/metaheat.R
MAMA/R/metagene.R
MAMA/R/MetaArrayclass2.r
MAMA/R/MCtest.R
MAMA/R/MAPsig2.R
MAMA/R/MAPsig1.R
MAMA/R/MAPmatrix.R
MAMA/R/MAP.R
MAMA/R/MAP.genes.R
MAMA/R/make.matrix.R
MAMA/R/join.results.R
MAMA/R/join.DEG.R
MAMA/R/gene.list.R
MAMA/R/entitybuild2.R
MAMA/R/dataZnew.R
MAMA/R/DataHandling.R
MAMA/R/cv.filter.R
MAMA/R/conting.tab.R
MAMA/R/compute.RQ.R
MAMA/R/clinical.sum.R
MAMA/NAMESPACE
MAMA/man
MAMA/man/zScores.Rd
MAMA/man/Z.Rd
MAMA/man/VennMapper.Rd
MAMA/man/test.group.shuffle.Rd
MAMA/man/T.select.Rd
MAMA/man/sigScore.Rd
MAMA/man/selectGenes.Rd
MAMA/man/selectClass.Rd
MAMA/man/selectAlpha.Rd
MAMA/man/sd.filter.Rd
MAMA/man/ratio.Rd
MAMA/man/RankProduct.Rd
MAMA/man/rank.genes.Rd
MAMA/man/rank.genes.adv.Rd
MAMA/man/RandomScore.Rd
MAMA/man/probs.to.matrix.Rd
MAMA/man/preparePermutations.Rd
MAMA/man/prepareData.Rd
MAMA/man/prelimScore.Rd
MAMA/man/posterior.mean.rd
MAMA/man/plotQvsChi.Rd
MAMA/man/plotpattern.Rd
MAMA/man/plotgene2.Rd
MAMA/man/plotgene.Rd
MAMA/man/plotES.Rd
MAMA/man/plot.SOGLresult.Rd
MAMA/man/performSOGL.Rd
MAMA/man/patternToString.Rd
MAMA/man/patternmatrix.Rd
MAMA/man/patternMatch.strong.Rd
MAMA/man/patternMatch.Rd
MAMA/man/METRADISC.Rd
MAMA/man/methods.Rd
MAMA/man/metaMA.Rd
MAMA/man/metalist.to.matrix.Rd
MAMA/man/metaheat2.Rd
MAMA/man/metaheat.Rd
MAMA/man/metagene.Rd
MAMA/man/MetaArray.Rd
MAMA/man/meta.test.Rd
MAMA/man/mergeExprs2.rd
MAMA/man/mergedata.Rd
MAMA/man/MCtest.Rd
MAMA/man/MAPsig2.Rd
MAMA/man/MAPsig1.Rd
MAMA/man/MAPmatrix.Rd
MAMA/man/MAP.Matches.Rd
MAMA/man/MAP.genes.Rd
MAMA/man/make.matrix.Rd
MAMA/man/join.results.Rd
MAMA/man/join.DEG.Rd
MAMA/man/gene.select.FC.Rd
MAMA/man/gene.list.Rd
MAMA/man/fold.change.Rd
MAMA/man/flip.Rd
MAMA/man/ES.GeneMeta.Rd
MAMA/man/entitybuild2.Rd
MAMA/man/cv.filter.Rd
MAMA/man/conting.tab.Rd
MAMA/man/computeOrdering.Rd
MAMA/man/computeAlpha.Rd
MAMA/man/compute.RQ.Rd
MAMA/man/commonGenes.Rd
MAMA/man/ColonData.Rd
MAMA/man/colIntersect.Rd
MAMA/man/clinical.sum.Rd
MAMA/man/clinical.Rd
MAMA/inst
MAMA/inst/doc
MAMA/inst/doc/MAMA.rnw
MAMA/inst/doc/MAMA.pdf
MAMA/DESCRIPTION
MAMA/data
MAMA/data/ColonData.RData