Integrate microRNA and gene expression to decipher pathway complexity


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Documentation for package ‘MIRit’ version 1.3.0

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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