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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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