Initial release submitted to Bioconductor.
loadHostData(): Import and normalize bulk RNA-seq count data using
TMM normalization and limma-voom precision weights. Returns a
SummarizedExperiment with both raw counts and voom-transformed values.
loadMicrobiomeData(): Import and normalize microbiome taxa tables using
centered log-ratio (CLR) or total sum scaling (TSS) transformation,
with automatic zero-inflation handling via pseudocounts. Returns a
SummarizedExperiment.
matchSamples(): Identify and retain paired samples present in both
host and microbiome datasets. Returns a MultiAssayExperiment.
jointDimReduction(): Run sparse multi-block PLS-DA (DIABLO from
mixOmics) for joint dimensionality reduction across host and microbiome
data layers. Returns integrated sample scores and feature loadings.
biomarkerDiscovery(): Identify top host genes and microbial taxa using
DIABLO sparse loadings and cross-omics Spearman correlation networks.
Returns a ranked DataFrame of multi-omics biomarkers.
diagnosticClassifier(): Train and evaluate host-only, microbiome-only,
and joint Random Forest classifiers using stratified k-fold cross-validation.
Provides AUC-ROC comparison quantifying the multi-omics advantage.
MultiOmicsBridgeAnalysis(): One-call wrapper executing the full
pipeline from matched MultiAssayExperiment through classification.
plotIntegration(): Joint biplot of sample scores in integrated
component space with feature loading vectors.
plotBiomarkerNetwork(): Clustered heatmap of host gene to microbial
taxon cross-omics Spearman correlations.
plotClassifierComparison(): ROC curves comparing host-only,
microbiome-only, and joint classifier performance.
plotSankey(): Feature-flow diagram from omics layer through selected
biomarkers to outcome classes.
generateReport(): Print or save a structured text summary of all
analysis results.
MOBResult S4 class with slots for integrated scores, feature loadings,
biomarker table, classifier performance, and parameters. Accessor
methods: biomarkers(), performance(), integrationScores(),
featureLoadings().