get_samp_class {ssMutPA}

Determining cancer subtypes using unsupervised spectral clustering algorithm.

Description

The function 'get_samp_class' using spectral clustering algorithm to obtain cancer subtype labels.

Usage

get_samp_class(
  Path_ES,
  sur,
  seed_num = 50,
  cox_pval = 0.05,
  min.nc = 2,
  max.nc = 5
)

Arguments

Path_ES

Single-sample mutation-based pathway enrichment score(ssMutPES) profiles.The file can be generated by the function 'get_RWR_ES'.

sur

A matrix containing the samples' survival time and survival states.

seed_num

The number of seeds for iterating to select the optimal clustering result.

cox_pval

A custom threshold to filter characteristic pathways, default to 0.05.

min.nc

Minimal number of clusters.

max.nc

maximal number of clusters,greater or equal to min.nc.

Value

A list containing the filtered pathways,the best seed for clustering,and cancer subtyoe labels .

Examples

#load the data.
surv_path <- system.file("extdata","sur.Rdata",package = "ssMutPA")
load(surv_path)
data(Path_ES)
#perform function `get_samp_class`.

res<-get_samp_class(Path_ES,sur,seed_num=5,cox_pval=0.05,min.nc = 2,max.nc =5)