FastSEAscore            Calculate the enrichment score of the pathways
                        .
MRWR                    A global propagation algorithm, random walk
                        with restart (RWR), to predict probable
                        influence of nodes in the network by seed
                        nodes.
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.
Seeds_Score             Seeds_Score The local weight of seed nodes.
cox_data                cox_data Univariate cox proportional hazards
                        regression data.
dot_data                dot_data A data frame.
dotplot                 Plotting the Dot plot.
get_RWR_ES              Calculate the single-sample mutation-based
                        pathway enrichment score.
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_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.
mut_onco                mut_onco A binary mutation matrix.
mut_status              mut_status A binary mutation matrix.
samp_class_onco         samp_class_onco
sample_class            sample_class The subtype labels of samples.
sur_onco                sur_onco
