Man pages for jordirofes/OmniOmics
Analysis of metabolomics (LC-MS) and transcriptomics (Microarray) data
| annotateData | Annotate Data |
| batchNormalization | Batch Normalization |
| compPlot | Feature comparison plot |
| featureBatchPVCA | PVCA batch effect plot |
| featurebatchQc | Feature sum intensity plot |
| featureSelection | Feature Selection |
| featureSign | Feature Sign |
| featureVarPlot | Variance Plot |
| geneFeatureFilter | Gene Feature Filter |
| ggChromPlot | Chromatogram plot |
| ggDensityPlot | Microarray intensity density plot |
| ggExprDistrPlot | Microarray intensity distribution boxplot/violin plot |
| ggPCAplot | Microarray sample PCA plot |
| ggTicQuality | Total ion count plot |
| groupComp | Basic group comparison |
| groupFeatureComp | Limma group comparison |
| groupFeatureVolcano | Volcano plot |
| heatmapPlot | Heatmap plot |
| loadingsPlot | Loadings Plot |
| metabFeatureFilter | Metablomics feature filter |
| metaboImport | Import metabolomics files .mzML/.mzXML |
| metaboProc | Metabolomics files process |
| mlFit | Caret model fitting |
| mlPredictCM | Caret confusion matrix |
| mlPredictROC | Receiver Operand Curve (ROC) |
| model.mat | Model matrix |
| multipca | Principal component analysis |
| pcaPlot | Principal component analysis plot |
| phenoImport | Import phenodata |
| procTranscript | Processing function for illumina and affymetrix microarrays... |
| transcriImport | Wrapper function for .idat, .cel and geoDatasets importing |
