#' @title A function to associate CNV generated by oncSNP starting from log R ratio and B allel frequences, generated by SNP arrays, to gene symbols
#' @description This function executes a ubuntu docker that uses as input the cnvs files produced by oncoSNP and add CN and LOH (check oncoSNP readme for more info) fields (rank 5 only) to the genes characterized by having genomics cohordinates included in the CNV region
#' @param group, a character string. Two options: sudo or docker, depending to which group the user belongs
#' @param genome.folder, a character string indicating the path of the folder where ENSEMBL genome.gtf is located, IMPORTANT use the same genome assembly used to design the array.
#' @param data.folder, a character string indicating the folder where input data (.cnvs) generated with oncoSNP are located and where output will be written
#' @author Raffaele Calogero, raffaele.calogero[at]unito[dot]it, University of Torino, Italy
#'
#' @return a file for each .cnvs, e.g. annotation_XXXX.cnvs.txt
#' @examples
#' \dontrun{
#' #running oncosnpAnnotation
#' system("wget http://130.192.119.59/public/test_oncosnp.zip")
#' system("unzip test_oncosnp.zip")
#' oncosnpAnnotation(group="docker", data.folder="./test_oncosnp/oncosnp_out", genome.folder="./test_oncosnp/hg19")
#' }
#'
#' @export
oncosnpAnnotation <- function(group=c("sudo","docker"), data.folder, genome.folder){
#storing the position of the home folder
home <- getwd()
#running time 1
ptm <- proc.time()
#setting the data.folder as working folder
if (!file.exists(data.folder)){
cat(paste("\nIt seems that the ",data.folder, " folder does not exist\n"))
return(2)
}
setwd(data.folder)
#initialize status
system("echo 0 > ExitStatusFile 2>&1")
#testing if docker is running
test <- dockerTest()
if(!test){
cat("\nERROR: Docker seems not to be installed in your system\n")
system("echo 10 > ExitStatusFile 2>&1")
setwd(home)
return(10)
}
#check if genome folder exist
if (!file.exists(genome.folder)){
cat(paste("\nIt seems that the ",genome.folder, " folder does not exist\n"))
system("echo 3 > ExitStatusFile 2>&1")
setwd(home)
return(3)
}
#executing the docker job
params <- paste("--cidfile ",data.folder,"/dockerID -v ",genome.folder,":/index -v ", data.folder, ":/data -d docker.io/repbioinfo/r340.2017.01 Rscript /bin/annotating_oncosnp.R", sep="")
resultRun <- runDocker(group=group, params=params)
#waiting for the end of the container work
if(resultRun==0){
cat("\nAnalysis is finished\n")
}
#running time 2
ptm <- proc.time() - ptm
dir <- dir(data.folder)
dir <- dir[grep("run.info",dir)]
if(length(dir)>0){
con <- file("run.info", "r")
tmp.run <- readLines(con)
close(con)
tmp.run[length(tmp.run)+1] <- paste("user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}else{
tmp.run <- NULL
tmp.run[1] <- paste("run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}
#saving log and removing docker container
container.id <- readLines(paste(data.folder,"/dockerID", sep=""), warn = FALSE)
system(paste("docker logs ", substr(container.id,1,12), " &> ",data.folder,"/", substr(container.id,1,12),".log", sep=""))
# system(paste("docker rm ", container.id, sep=""))
#removing temporary data
system("rm -fR dockerID")
system(paste("cp ",paste(path.package(package="docker4seq"),"containers/containers.txt",sep="/")," ",data.folder, sep=""))
setwd(home)
}
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