| calculatePermutedScoreByGeneSampling | Calculate the permuted latent trait by gene sampling |
| CN_N | Ovarian Cancer Datasets |
| CN_T | Ovarian Cancer Datasets |
| computeAbility | Calculate latent traits for a given response matrix and item parameters using MLE |
| dichotomize | A wrapper that is able to dichotomize expression, methylation and CN data |
| dichotomizeCN | Dichotomizing copy number data based on segmented data (i.e. log2ratio). |
| dichotomizeExpr | Dichotomize the expression data given both tumor and normal samples. |
| dichotomizeMethy | Dichotomize the methylation data given both tumor and normal controls. |
| Expr_N | Ovarian Cancer Datasets |
| Expr_T | Ovarian Cancer Datasets |
| fitOnSinglePlat | Fit IRT model on a single platform |
| intIRTeasyRun | The easyrun function for integrating multiple modalities of high throughput assays using binary input matrix. |
| intIRTeasyRunFromRaw | The easyrun function for integrating multiple modalities of high throughput assays using raw data. |
| Methy_N | Ovarian Cancer Datasets |
| Methy_T | Ovarian Cancer Datasets |
| OV | Ovarian Cancer Datasets |
| simulateBinaryResponseMat | Simulate binary response matrix according to 2-parameter Item Characteristic Function for given latent traits and item parameters. |