MAMA: Meta-Analysis of MicroArray

Implementation of methods for microarray meta-analysis.

AuthorIvana Ihnatova <184415@mail.muni.cz>.
Date of publication2013-04-30 06:22:29
MaintainerIvana Ihnatova <184415@mail.muni.cz>
LicenseGPL (>= 2)
Version2.2.1

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

Functions

as.list,MetaArray-method Man page
clinical Man page
clinical<- Man page
clinical<-, MetaArray-method Man page
clinical<-,MetaArray-method Man page
clinical<-MetaArray-method Man page
clinical<--methods Man page
clinical.sum Man page
colIntersect Man page
ColonData Man page
commonGenes Man page
computeAlpha Man page
computeOrdering Man page
compute.RQ Man page
conting.tab Man page
cv.filter Man page
datanames Man page
datanames<- Man page
datanames<-, MetaArray-method Man page
datanames<-,MetaArray-method Man page
datanames<-MetaArray-method Man page
datanames<--methods Man page
entitybuild2 Man page
ES.GeneMeta Man page
ES.GeneMeta.res Man page
flip Man page
fold.change Man page
GEDM Man page
GEDM<- Man page
GEDM<-, MetaArray-method Man page
GEDM<-, MetaArray-method Man page
GEDM<-,MetaArray-method Man page
GEDM<--methods Man page
gene.list Man page
gene.select.FC Man page
join.DEG Man page
join.results Man page
make.matrix Man page
MAP.genes Man page
MAP.Matches Man page
MAP.Matches.res Man page
MAPmatrix Man page
MAPsig1 Man page
MAPsig2 Man page
MCtest Man page
mergedata Man page
MetaArray-class Man page
metagene Man page
metaheat Man page
metaheat2 Man page
metalist.to.matrix Man page
metaMA Man page
metaMA.res Man page
meta.test Man page
METRADISC Man page
METRADISC.res Man page
multExpFDR Man page
patternMatch Man page
patternMatch.strong Man page
patternmatrix Man page
patternToString Man page
performSOGL Man page
plotES Man page
plotgene Man page
plotgene2 Man page
plot,MetaArray,ANY-method Man page
plot,MetaArray,missing-method Man page
plotpattern Man page
plotQvsChi Man page
plot.SOGLresult Man page
prelimScore Man page
prepareData Man page
preparePermutations Man page
print,MetaArray-method Man page
probs.to.matrix Man page
RandomScore Man page
rank.genes Man page
rank.genes.adv Man page
RankProduct Man page
RankProduct.res Man page
ratio Man page
sd.filter Man page
selectAlpha Man page
selectClass Man page
selectGenes Man page
show,MetaArray-method Man page
sigScore Man page
test.group.shuffle Man page
T.select Man page
VennMapper Man page
VennMapper.res Man page
Z Man page
zScoreFDR Man page
zScorePermuted Man page
zScores Man page

Files

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

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