MetaIntegrator: Meta-Analysis of Gene Expression Data
Version 1.0.3

A pipeline for the meta-analysis of gene expression data. We have assembled several analysis and plot functions to perform integrated multi-cohort analysis of gene expression data (meta- analysis). Methodology described in: .

Browse man pages Browse package API and functions Browse package files

AuthorWinston A. Haynes, Francesco Vallania, Aurelie Tomczak, Timothy Sweeney, Erika Bongen, Purvesh Khatri
Date of publication2016-09-29 08:02:32
MaintainerWinston A. Haynes <hayneswa@stanford.edu>
LicenseLGPL
Version1.0.3
URL http://biorxiv.org/content/early/2016/08/25/071514
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MetaIntegrator")

Man pages

backwardSearch: Backward Search Function
calculateROC: Calculate ROC Curve Statistics
calculateScore: Calculate a signature Z-score for a set of genes in a single...
checkDataObject: Check for errors in objects used for analysis
ens_ensgID_table: ENSEMBL gene id table cache
ens_entrez_table: ENSEMBL entrez table cache
filterGenes: Filter out significant genes from meta-analysis results
forestPlot: Compare effect sizes of a gene across all datasets in...
forwardSearch: Forward Search Function
getGEOData: GEO download/processing through GEOquery
getMostRecentFilter: Get name of most recent filter
getSampleLevelGeneData: Extract gene-level data from a given data object
heatmapPlot: Generates a heatmap with effect sizes for all genes which...
metaIntegrator_public-package: MetaIntegrator package for meta-analysis of gene expression...
regressionPlot: Generate a plot which draws a regrssion line between the Meta...
rocPlot: Plot ROC Curve for a Dataset
runMetaAnalysis: Run the meta-analysis algorithm
summarizeFilterResults: Summarize the filtered analysis results
tinyMetaObject: A Tiny MetaObject
ucsc_genbank_table: UCSC genbank table cache
ucsc_refseq_table: UCSC refseq table cache
violinPlot: Compare groups within a single dataset in a violin plot

Functions

GEM_inf_gene_remover Source code
GEM_log_check_v1 Source code
GEO_fData_key_parser Source code
GEOqueryCreateGEM Source code
GEOqueryGEO2GEM Source code
MetaIntegrator Man page
backSearchWeighted Source code
backsearchInner Source code
backsearchNeg Source code
backsearchPos Source code
backwardSearch Man page Source code
calculateROC Man page Source code
calculateScore Man page Source code
check.metaGEM.study Source code
checkClass Source code
checkDataObject Man page Source code
checkType Source code
classVectorChecker Source code
cleanNA Source code
combine.effect.sizes Source code
combine.significances Source code
convertDiscoveryListToGenes Source code
createAnnTable Source code
createRegressionPlot Source code
createViolinPlot Source code
datasetCheckAll Source code
datasetCheckExpr Source code
datasetCheckKeys Source code
datasetCheckNull Source code
datasetCheckRowColNames Source code
datasetCheckType Source code
effect.sizes Source code
ens_ensgID_table Man page
ens_entrez_table Man page
ensembl_ensgID_table Source code
ensembl_entrez_connector Source code
ensembl_entrez_table Source code
ensembl_gene_connector_hs76 Source code
expand.df Source code
extractDataFromGEM Source code
filterGenes Man page Source code
filterMetaRun Source code
forestPlot Man page Source code
forwardSearch Man page Source code
forwardSearchInner Source code
forwardSearchNeg Source code
forwardSearchPos Source code
forwardSearchWeighted Source code
geomMean Source code
geoquery_gems_2_singlelist Source code
get.ttest.P Source code
getAUCsGenesList Source code
getES Source code
getGEOData Man page Source code
getGenesData Source code
getMostRecentFilter Man page Source code
getSampleLevelGeneData Man page Source code
getWeightedAUCsGenesList Source code
heatmapPlot Man page Source code
leaveOneOutMetaAnalysisWrapper Source code
matchAll Source code
metaAnalysisCheckNull Source code
metaAnalysisCheckType Source code
metaCheckAll Source code
metaCheckNull Source code
metaCheckType Source code
metaFilterCheckNull Source code
metaFilterCheckType Source code
multimerge Source code
originalDataNameChecker Source code
originalDataNameConverter Source code
pool.inverseVar Source code
regressionPlot Man page Source code
replaceNAs Source code
replaceNaNs Source code
replaceValues Source code
rocPlot Man page Source code
rocplot.single Source code
runMetaAnalysis Man page Source code
runMetaAnalysisCore Source code
scoreGenesMtx Source code
sum.of.logs Source code
summ.eff.within Source code
summ.sigs.within Source code
summarizeFilterResults Man page Source code
tinyMetaObject Man page
ttest.Pvalues Source code
ttest.Qvalues Source code
ucsc_genbank_connector_hg19 Source code
ucsc_genbank_table Man page Source code
ucsc_refseq_connector_hg19 Source code
ucsc_refseq_table Man page Source code
violinPlot Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/MetaIntegrator.R
inst/doc/MetaIntegrator.html
inst/doc/MetaIntegrator.Rmd
inst/unitTests
inst/unitTests/testOutput
inst/unitTests/testOutput/temp.temp
inst/unitTests/test_backwardSearch.R
inst/unitTests/test_rocPlot.R
inst/unitTests/test_filterGenes.R
inst/unitTests/goldStandardOutput
inst/unitTests/goldStandardOutput/violinPlots.pdf
inst/unitTests/goldStandardOutput/rocPlots.pdf
inst/unitTests/goldStandardOutput/forestPlots.pdf
inst/unitTests/test_forwardSearch.R
inst/unitTests/test_checkDataObject.R
inst/unitTests/test_summarizeFilterResults.R
inst/unitTests/test_calculateROC.R
inst/unitTests/test_getSampleLevelGeneData.R
inst/unitTests/test_getMostRecentFilter.R
inst/unitTests/test_runMetaAnalysis.R
inst/unitTests/test_forestPlot.R
inst/unitTests/test_calculateScore.R
inst/unitTests/test_violinPlot.R
tests
tests/runTests.R
NAMESPACE
NEWS
data
data/ucsc_refseq_table.rda
data/ucsc_genbank_table.rda
data/tinyMetaObject.RData
data/datalist
data/ens_entrez_table.rda
data/ens_ensgID_table.rda
R
R/ROC_and_search_functions.R
R/checkDataObject.R
R/metaIntegrator_public.R
R/metaAnalysis.R
R/summarizeFilterResults.R
R/getMostRecentFilter.R
R/heatmapPlot.R
R/getGEOData.R
R/calculateScore.R
R/checkDataObject_functions.R
R/filterGenes.R
R/metaAnalysisFoundation.R
R/runMetaAnalysis.R
R/violinPlot.R
R/regressionPlot.R
R/forestPlot.R
R/getSampleLevelGeneData.R
vignettes
vignettes/images
vignettes/images/Eq3.png
vignettes/images/Eq1.png
vignettes/images/schema_simplified.pdf
vignettes/images/schema_simplified2.png
vignettes/images/Eq4.png
vignettes/images/Eq2.png
vignettes/MetaIntegrator.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/getGEOData.Rd
man/calculateScore.Rd
man/checkDataObject.Rd
man/runMetaAnalysis.Rd
man/regressionPlot.Rd
man/ucsc_genbank_table.Rd
man/ens_ensgID_table.Rd
man/summarizeFilterResults.Rd
man/ucsc_refseq_table.Rd
man/forwardSearch.Rd
man/backwardSearch.Rd
man/getMostRecentFilter.Rd
man/forestPlot.Rd
man/ens_entrez_table.Rd
man/rocPlot.Rd
man/tinyMetaObject.Rd
man/heatmapPlot.Rd
man/violinPlot.Rd
man/calculateROC.Rd
man/getSampleLevelGeneData.Rd
man/metaIntegrator_public-package.Rd
man/filterGenes.Rd
MetaIntegrator documentation built on May 19, 2017, 4:50 p.m.