A function to handle a docker containier preparing the file needed for expanse

This function executes a ubuntu docker that produces the cnv.txt and snv.txt needed for expanse

prepare4expands(group = c("sudo", "docker"), data.folder)

Arguments

group,

a character string. Two options: sudo or docker, depending to which group the user belongs
data.folder,

a character string indicating the folder where input data are located and where output will be written

Value

cnv.txt and snv.txt

Examples

if (FALSE) {
    system("wget http://130.192.119.59/public/prepare4expanse.zip")
    system("unzip prepare4expanse.zip")
    prepare4expands(group="docker", data.folder=paste(getwd(), "prepare4expanse", sep="/"))
}