get_sam_cla {PMAPscore}

get_sam_cla

Description

Function 'get_sample_classification' This function is used to judge the classification of samples.

Usage

get_sam_cla(
  mut_sam,
  gene_Ucox,
  symbol_Entrez,
  path_cox_data,
  sur,
  path_Ucox_mul,
  sig,
  cut_off = -0.986,
  data.dir = NULL,
  organism = "hsa",
  TRAIN = FALSE
)

Arguments

mut_sam

The sample somatic mutation data.

gene_Ucox

Results of gene univariate Cox regression.

symbol_Entrez

A data table containing gene symbol and gene Entrez ID.

path_cox_data

Pathways of Cancer-specifical obtained from the training set.

sur

This data contains survival status and survival time of each sample.

path_Ucox_mul

Multivariate Cox regression results of Cancer-specifical pathways.

sig

Cancer-specific dysregulated signal pathways. It can be generated by the function 'get_final_signature'.

cut_off

Threshold of classification.

data.dir

Location of the "organism"SPIA.RData file containing the pathways data. If set to NULL will look for this file in the extdata folder of the PMAPscore library.

organism

A three letter character designating the organism. See a full list at ftp://ftp.genome.jp/pub/kegg/xml/organisms.

TRAIN

Logical,if set FLASE,we need to load the result of multivariate Cox regression of cancer specific pathways into the training set.

Value

Return a data frame, the sample's risk score and the sample's risk group.

Examples

#Load the data.
data(mut_sam,gene_Ucox,symbol_Entrez,path_cox_data,sur,path_Ucox_mul)
#perform function `get_sample_cla`.
get_sam_cla(mut_sam,gene_Ucox,symbol_Entrez,path_cox_data,sur,path_Ucox_mul,sig,cut_off=-0.986)