MetaIntegrator          MetaIntegrator package for meta-analysis of
                        gene expression data
backwardSearch          Backward Search Function
calcMetaPower           Calculates the statistical power of a random
                        effects meta-analysis
calculateROC            Calculate ROC Curve Statistics
calculateScore          Calculate a signature Z-score for a set of
                        genes in a single dataset
checkDataObject         Check for errors in objects used for analysis
classFunction           Helper function to build the class vector
cleanUpPheno            Automatic preprocessing of $pheno dataframe
coconutMetaIntegrator   A wrapper function to run COCONUT on the
                        MetaIntegrator objects.
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 meta-analysis
forwardSearch           Forward Search Function
geneSymbolCorrection    Correct/update gene symbols in a metaObject
getGEOData              GEO download/processing through GEOquery
getMostRecentFilter     Get name of most recent filter
getSampleLevelGeneData
                        Extract gene-level data from a given data
                        object
ggForestPlot            Compare effect sizes of a gene across all
                        datasets in meta-analysis
heatmapPlot             Generates a heatmap with effect sizes for all
                        genes which pass a filter in all measured
                        diseases
immunoStatesDecov       immunoStates deconvolution analysis on
                        MetaIntegrator object(s)
immunoStatesGenePropCorr
                        Correct gene expression using cell proportions
                        from immunoStates
immunoStatesMatrix      immunoStates basis matrix
immunoStatesMeta        immunoStates deconvolution analysis on
                        MetaIntegrator object(s)
imputeSex               Imputes biological sex of each sample in a
                        Dataset object
lincsBaitCorr           Run Shane's LINCS bait-based correlation on
                        MetaIntegrator
lincsCorrelate          Run Shane's LINCS Correlate on MetaIntegrator
lincsTools              Run Shane's LINCS Tools on MetaIntegrator
manhattanPlot           Generates a Manhattan plot with effect size FDR
                        as y-axis
multiplePRCPlot         Generate a plot with multiple PRC curves
multipleROCPlot         Generate a plot with multiple ROC curves
pooledROCPlot           Generate a plot with a pooled ROC curve
prcPlot                 Plot the PRC Curve for a Dataset
predvalPlot             Plot positive and negative predictive values
                        across different prevalences
regressionPlot          Generate a plot which draws a regression line
                        between the Meta Score and a continuous
                        variable phenotype.
rocPlot                 Plot ROC Curve for a Dataset
runMetaAnalysis         Run the meta-analysis algorithm
subsetOriginalData      Subset samples for a particular dataset
summarizeFilterResults
                        Summarize the filtered analysis results
summaryROCCalc          Calculate the summaryROC statistics
summaryROCPlot          Generate a plot with a summary ROC curve
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
