Extract the gene set list from the background model

Description

Usage

as.geneSet(background);

Arguments

Details

the result list could be used for save as json file for parsed in R by jsonlite::fromJSON function, and used for the gsva analysis.

Authors

Value

a tuple list object that contains the gene set information, data result in format like:

 list(
     "cluster id 1" = c("gene id", "gene id", ...),
     "cluster id 2" = c("gene id", "gene id", ...),
     ...
 )

clr value class

• list

Examples

 let kb = read.background("hsa.xml");
 let geneSet = as.geneSet(kb);
 
 # save as json file
 geneSet 
 |> JSON::json_encode()
 |> writeLines(con = "hsa.json")
 ;
 
 # load in R
 library(jsonlite);
 geneSet = jsonlite::fromJSON("hsa.json");
 
 # use for gsva analysis
 gsva(data, geneSet, method="gsva", ...);