# Single-Sample Mutation-Based Pathway Analysis

## Documentation for package ‘ssMutPA’ version 0.1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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