Man pages for bkaczkowski/xcore
xcore expression regulators inference
| addSignatures | Add molecular signatures to MultiAssayExperiment |
| applyOverColumnGroups | Apply function over groups of columns |
| applyOverDFList | Apply function over selected column in list of data frames |
| design2factor | Transform design matrix to factor |
| estimateStat | Estimate linear models goodness of fit statistic |
| filterSignatures | Filter signatures by coverage |
| fisherMethod | Combine p-values using Fisher method |
| getCoverage | Calculate regions coverage |
| getInteractionMatrix | Compute interaction matrix |
| getVarianceWeightedAvgCoeff | Calculate variance weighted average coefficients matrix |
| isTRUEorFALSE | Check if argument is a binary flag |
| mae | Calculate Mean Absolute Error |
| maeSummary | Helper summarizing MAE object |
| modelGeneExpression | Gene expression modeling pipeline |
| modelGeneExpression_ridge_regression_wraper | Ridge regression wrapper for modelGeneExpression |
| modelGeneExpression_significance_testing_wraper | Statistical testing of ridge regression estimates wrapper for... |
| mse | Calculate Mean Squared Error |
| pipe | re-export magrittr pipe operator |
| prepareCountsForRegression | Process count matrix for expression modeling |
| regressionData | Create MultiAssayExperiment object for expression modeling |
| remap_mini | xcore example molecular signatures |
| repVarianceWeightedAvgZscore | Calculate replicate variance weighted averaged Z-scores |
| ridgePvals | Significance testing in linear ridge regression |
| rinderpest_mini | xcore example expression data |
| rsq | Calculate $R^2$ |
| simplifyInteractionMatrix | Simplify Interaction Matrix |
| stoufferZMethod | Combine Z-scores using Stouffer's method |
| subsetWithMissing | Subset keeping missing |
| translateCounts | Translate counts matrix rownames |
