Single-Sample Mutation-Based Pathway Analysis

Documentation for package ‘ssMutPA’ version 0.1.2

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