Man pages for IntLIM
Integration of Omics Data Using Linear Modeling
| BuildDataAndLines | A helper function for the PlotPair functions (i.e. the... |
| CreateCrossValFolds | Creates multiple cross-validation folds from the data. Format... |
| DistPvalues | Visualize the distribution of unadjusted p-values from linear... |
| DistRSquared | Visualize the distribution of unadjusted p-values from linear... |
| FilterData | Filter input data by abundance values and number of missing... |
| FilterDataFolds | Filter input data by abundance values (analyte data) and... |
| getQuantileForInteractionCoefficient | Function that gets numeric cutoffs from percentile |
| getStatsAllLM | Function that runs Linear Models for all analytes |
| getstatsOneLM | Function that runs linear models for analyte vs. all analytes... |
| HistogramPairs | histogram of analyte pairs depending upon independent or... |
| InteractionCoefficientGraph | Graphs a scatterplot of pairs vs. the interaction coefficient... |
| IntLimData-class | IntLimData class |
| IntLIM-package | IntLIM: Integration of Omics Data Using Linear Modeling |
| IntLimResults-class | IntLimResults class |
| MarginalEffectsGraph | Creates a dataframe of the marginal effect of phenotype |
| MarginalEffectsGraphDataframe | Creates a dataframe of the marginal effect of phenotype |
| multi.which | A which for multidimensional arrays. Mark van der Loo... |
| OutputData | Output data into individual CSV files. All data will be... |
| OutputResults | Output results into a zipped CSV file. Results include gene... |
| PermutationCountSummary | Return the number of significant analytes and the number of... |
| PermutationPairSummary | Return the number of significant analytes / pairs per... |
| PermuteIntLIM | Run permutations of the IntLIM code to search for random... |
| PlotDistributions | Get some stats after reading in data |
| PlotFoldOverlapUpSet | Makes an UpSet plot showing the filtered pairs of analytes... |
| PlotPair | scatter plot of pairs (based on user selection) |
| PlotPairFlat | scatter plot of pairs (based on user selection). This version... |
| PlotPCA | PCA plots of data for QC |
| ProcessResults | Retrieve significant pairs, based on adjusted p-values. For... |
| ProcessResultsAllFolds | Retrieve significant pairs, based on adjusted p-values,... |
| ProcessResultsContinuous | Retrieve significant pairs (aka filter out nonsignificant... |
| pvalCoefVolcano | 'volcano' plot (difference in correlations vs p-values) of... |
| PValueBoxPlots | Visualize the distribution of unadjusted p-values for all... |
| ReadData | Read in CSV file |
| RemovePlusInCovars | RemovePlusInCovars |
| RunCrossValidation | Runs the cross-validation end-to-end using the following... |
| RunIntLim | Run linear models and retrieve relevant statistics |
| RunIntLimAllFolds | Run linear models for all data folds. This is a wrapper to... |
| runIntLIMApp | run shiny app |
| RunLM | Function that runs linear models and returns interaction... |
| ShowStats | Get some stats after reading in data |
