| cox_data | cox_data Univariate cox proportional hazards regression data. |
| dotplot | Plotting the Dot plot. |
| dot_data | dot_data A data frame. |
| FastSEAscore | Calculate the enrichment score of the pathways . |
| get_heatmap | Plotting a heatmap with subtype labels. |
| get_indicate | Indicator function. |
| get_mut_status | Converts MAF file or data in other formats into mutation matrix. |
| get_RWR_ES | Calculate the single-sample mutation-based pathway enrichment score. |
| get_samp_class | Determining cancer subtypes using unsupervised spectral clustering algorithm. |
| get_seeds_score | Calculate the local wight of seed nodes. |
| get_univarCox_result | Perform the univariate Cox proportional hazards regression analysis. |
| mountain_plot | Plotting the density ridges plot. |
| MRWR | A global propagation algorithm, random walk with restart (RWR), to predict probable influence of nodes in the network by seed nodes. |
| mut_onco | mut_onco A binary mutation matrix. |
| mut_status | mut_status A binary mutation matrix. |
| Oncoplot | Drawing a waterfall plot of a particular pathway. |
| Path_ES | Path_ES Single-sample mutation-based pathway enrichment score profiles. |
| Path_Name | Path_Name |
| RWR_res | RWR_res Random walk results based on mutated genes in a single sample. |
| sample_class | sample_class The subtype labels of samples. |
| samp_class_onco | samp_class_onco |
| Seeds_Score | Seeds_Score The local weight of seed nodes. |
| sur_onco | sur_onco |