# Integrate microRNA and gene expression to decipher pathway complexity

## Documentation for package ‘MIRit’ version 1.4.0

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

## Help Pages

addDifferentialExpression | Manually add differential expression results to a MirnaExperiment object
augmentedPathways | Access the miRNA-augmented pathways that were used during TAIPA
augmentedPathways-method | The 'IntegrativePathwayAnalysis' class
batchCorrection | Correct for batch effects in miRNA and gene expression measurements
deAccessors | Extract differentially expressed miRNAs and genes from a 'MirnaExperiment' object
deAnalysis | Perform differential expression analysis
enrichedFeatures | Extract the names of the pre-ranked features in a GSEA experiment
enrichedFeatures-method | The 'FunctionalEnrichment' class
enrichGenes | Perform functional enrichment analysis of genes
enrichmentBarplot | Create a barplot for functional enrichment analysis
enrichmentDatabase | Access the database used for functional enrichment analyses
enrichmentDatabase-method | The 'FunctionalEnrichment' class
enrichmentDotplot | Create a dotplot for functional enrichment analysis
enrichmentMethod | Access the method used for functional enrichment analyses
enrichmentMethod-method | The 'FunctionalEnrichment' class
enrichmentMetric | Extract the GSEA ranking metric used for functional enrichment analyses
enrichmentMetric-method | The 'FunctionalEnrichment' class
enrichmentResults | Access the results of functional enrichment analyses
enrichmentResults-method | The 'FunctionalEnrichment' class
enrichTargets | Perform an enrichment analysis of integrated microRNA targets
findMirnaSNPs | Find disease-associated SNPs occurring at DE-miRNA loci
FunctionalEnrichment | The 'FunctionalEnrichment' class
FunctionalEnrichment-class | The 'FunctionalEnrichment' class
geneCounts | Count matrix for gene expression in thyroid cancer
geneDE | Extract differentially expressed miRNAs and genes from a 'MirnaExperiment' object
geneDE-method | The 'MirnaExperiment' class
geneSet | Extract the gene-sets used for functional enrichment analyses
geneSet-method | The 'FunctionalEnrichment' class
getEvidence | Get the scientific evidence for a particular disease-SNP association
getTargets | Get microRNA targets
gseaPlot | Create a GSEA plot that displays the running enrichment score (ES) for a given pathway
gseaRidgeplot | Create a ridgeplot to display the results of GSEA analysis
integratedPathways | Access the results of integrative miRNA-mRNA pathway analyses
integratedPathways-method | The 'IntegrativePathwayAnalysis' class
integration | Explore the results of the integration analysis between miRNAs and genes
integration-method | The 'MirnaExperiment' class
integrationDatabase | Extract the database used for integrative miRNA-mRNA pathway analyses
integrationDatabase-method | The 'IntegrativePathwayAnalysis' class
integrationDotplot | Display integrated miRNA-mRNA augmented pathways in a dotplot
IntegrativePathwayAnalysis | The 'IntegrativePathwayAnalysis' class
IntegrativePathwayAnalysis-class | The 'IntegrativePathwayAnalysis' class
listPathways | List all the available biological pathways in KEGG, Reactome and WikiPathways
loadExamples | Load example MIRit objects
mirnaCounts | Count matrix for microRNA expression in thyroid cancer
mirnaDE | Extract differentially expressed miRNAs and genes from a 'MirnaExperiment' object
mirnaDE-method | The 'MirnaExperiment' class
MirnaExperiment | The constructor function for MirnaExperiment
MirnaExperiment-class | The 'MirnaExperiment' class
mirnaIntegration | Integrate microRNA and gene expression
mirnaTargets | Explore miRNA-target pairs
mirnaTargets-method | The 'MirnaExperiment' class
mirVariantPlot | Create a trackplot to show the association between miRNAs and disease-SNPs
pairedSamples | View the relationship between miRNA and gene samples
pairedSamples-method | The 'MirnaExperiment' class
performGeneDE | Perform differential expression analysis
performMirnaDE | Perform differential expression analysis
plotCorrelation | Plot correlation between miRNAs and genes within biological groups
plotDE | Represent differentially expressed miRNAs/genes as boxplots, barplots or violinplots
plotDimensions | Generate multidimensional scaling (MDS) plots to explore miRNA/gene expression distances
plotVolcano | Produce volcano plots to display miRNA/gene differential expression
preparePathways | Prepare miRNA-augmented pathways for integrative miRNA-mRNA pathway analyses
searchDisease | Search for disease EFO identifiers
show-method | The 'FunctionalEnrichment' class
show-method | The 'IntegrativePathwayAnalysis' class
show-method | The 'MirnaExperiment' class
significantAccessors | Get the IDs of statistically differentially expressed miRNAs/genes
significantGenes | Get the IDs of statistically differentially expressed miRNAs/genes
significantGenes-method | The 'MirnaExperiment' class
significantMirnas | Get the IDs of statistically differentially expressed miRNAs/genes
significantMirnas-method | The 'MirnaExperiment' class
supportedOrganisms | Get the list of supported organisms for a given database
topologicalAnalysis | Perform a topologically-aware integrative pathway analysis (TAIPA)
visualizeNetwork | Visualize the relationships between miRNAs and genes in a biological pathway