Man pages for Mathelab/IntLIM
Integration of Omics Data Using Linear Modeling
| CorrHeatmap | Plot correlation heatmap |
| CorrHeatmap_pdf | Plot correlation heatmap in pdf |
| CreateIntLimObject | Generic function to create constructor of MultiDataSet gene... |
| DistPvalues | Visualize the distribution of unadjusted p-values from linear... |
| FilterData | Filter input data by abundance values (gene and metabolite... |
| getCommon | Function that returns a list of all data for samples in... |
| getGeneList | Obtain lists of source IDs for inputting into RaMP or other... |
| getMetabList | Obtain lists of source IDs for inputting into RaMP or other... |
| getstatsOneLM | Function that runs linear models for one gene vs all... |
| HistogramGMPairs | histogram of gene-metabolite pairs depending upon metabolite... |
| IntLimResults-class | IntLimResults class |
| MetaboliteSet-class | MetaboliteSet class extenstion for MultiDataSet object |
| OutputData | Output data into individual CSV files. All data will be... |
| OutputResults | Output results into a zipped CSV file. Results include gene... |
| PlotDistributions | Get some stats after reading in data |
| PlotGMPair | scatter plot of gene-metabolite pairs (based on user... |
| PlotPCA | PCA plots of data for QC |
| ProcessResults | Retrieve significant gene-metabolite pairs, based on adjusted... |
| pvalCorrVolcano | 'volcano' plot (difference in correlations vs p-values) of... |
| ReadData | Read in CSV file |
| RunIntLim | Run linear models and retrieve relevant statistics |
| runIntLIMApp | run shiny app |
| RunLM | Function that runs linear models and returns interaction... |
| ShowStats | Get some stats after reading in data |
