Meta-Analysis of Gene Expression Data

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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