#' @title A wrapper function for sample_size_distribution function from RnaSeqSampleSize Bioconductor package
#' @description This function executes sample_size_distribution to identify the number of samples x group needed to obtain a specific statistical power
#' @param group, a character string. Two options: \code{"sudo"} or \code{"docker"}, depending to which group the user belongs
#' @param filename, a character string indicating the name of the count table file
#' @param power, expected statistical power required to detect prognostic genes
#' @param FDR, false discovery rate
#' @param genes4dispersion, an integer indicating the number of genes used in estimation of read counts and dispersion distribution
#' @param log2fold.change, an integer indicating the minimum log2 fold change for prognostic genes between two groups
#' @param output.folder, a string indicating the path where to save the output file
#' @author Raffaele Calogero
#'
#' @return a string with the requested informations. the string is also saved in a file: sample_size_evaluation.txt , power_evaluation.txt
#' @examples
#'\dontrun{
#' system("wget 130.192.119.59/public/test.analysis.zip")
#' unzip("test.analysis.zip")
#' setwd("test.analysis")
#' library(docker4seq)
#' sampleSize(group="docker", filename="_counts.txt", power=0.80, FDR=0.1,
#' genes4dispersion=200, log2fold.change=1)
#'}
#' @export
sampleSize <- function(group=c("sudo","docker"), filename, power=0.80, FDR=0.1, genes4dispersion=200, log2fold.change=1, output.folder=getwd()){
#running time 1
ptm <- proc.time()
home <- getwd()
setwd(output.folder)
#initialize status
system("echo 0 > ExitStatusFile 2>&1")
#running time 1
test <- dockerTest()
if(!test){
cat("\nERROR: Docker seems not to be installed in your system\n")
#initialize status
system("echo 10 > ExitStatusFile 2>&1")
setwd(home)
return(10)
}
#removing the path from filename
filename.tmp <- unlist(strsplit(filename,'/'))
filename <- filename.tmp[length(filename.tmp)]
params <- paste("--cidfile ",output.folder, "/dockerID -v ",output.folder,":/data/scratch -d docker.io/repbioinfo/r332.2017.01 Rscript /bin/.sampleSize.R ", filename, " ", power, " ", FDR, " ", genes4dispersion, " ", log2fold.change, sep="")
resultRun <- runDocker(group=group, params=params)
if(resultRun==0){
cat("\nSample size analysis is finished\n")
}
#running time 2
ptm <- proc.time() - ptm
dir <- dir(output.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("sampleSize user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("sampleSize system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("sampleSize elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}else{
tmp.run <- NULL
tmp.run[1] <- paste("sampleSize user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("sampleSize system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("sampleSize elapsed run time mins ",ptm[3]/60, sep="")
}
writeLines(tmp.run,"run.info")
#saving log and removing docker container
container.id <- readLines(paste(output.folder,"/dockerID", sep=""), warn = FALSE)
# system(paste("docker logs ", container.id, " >& ", substr(container.id,1,12),".log", sep=""))
system(paste("docker logs ", container.id, " >& ","sampleSize_",substr(container.id,1,12),".log", sep=""))
# system(paste("docker rm ", container.id, sep=""))
system("rm -fR anno.info")
system("rm -fR dockerID")
system(paste("cp ",paste(path.package(package="docker4seq"),"containers/containers.txt",sep="/")," ",output.folder, sep=""))
setwd(home)
}
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