# Meta-Analysis of Gene Expression Data

## Documentation for package ‘MetaIntegrator’ version 2.1.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
MetaIntegrator | MetaIntegrator package for meta-analysis of gene expression data
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