get_pfs_score {PMAPscore}

Calculates the pathway-based mutation accumulate perturbation score

Description

The function 'get_pfs_score' uses to calculate the pathway-based mutation accumulate perturbation score using the matrix of gene mutation state and pathway information.

Usage

get_pfs_score(
  mut_status,
  percent,
  gene_Ucox_res,
  gene_symbol_Entrez,
  data.dir = NULL,
  organism = "hsa",
  verbose = TRUE,
  Entrez_ID = TRUE,
  gene_set = NULL
)

Arguments

mut_status

Mutation status of a particular gene in a particular sample. The file can be generated by the function 'get_mut_status'.

percent

This parameter is used to control the mutation rate of gene. Genes less than this value will be deleted

gene_Ucox_res

Results of gene univariate Cox regression.

gene_symbol_Entrez

A data table containing gene symbol and gene Entrez ID.

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 PFS library.

organism

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

verbose

If set to TRUE, displays the number of pathways already analyzed.

Entrez_ID

Logical,tell whether there are Entrez IDs corresponding to gene symbol in the gene_symbol_Entrez.

gene_set

A group of cancer specific gene symbols obtained from the training set

Value

A binary mutations matrix, which column names is sample and the row name is the pathway.

Examples

#get the path of the mutation annotation file.
data(mut_status,gene_Ucox_res,gene_symbol_Entrez)
#perform the function `get_pfs_score`.
pfs_score<-get_pfs_score(mut_status[,1:2],percent=0.03,gene_Ucox_res,gene_symbol_Entrez)