#' @title A function allowing the identification of differentially expressed genes.
#' @description This function executes in a docker edgeR for the idnetification of differentially expressed genes in single-cells RNAseq
#' @param group, a character string. Two options: sudo or docker, depending to which group the user belongs
#' @param data.folder, a character string indicating the folder where input data are located and where output will be written
#' @param counts.table, a character string indicating the counts table file. IMPORTANT in the header of the file the covariate group MUST be associated to the column name using underscore, e.g. cell1_cov1
#' @param file.type, type of file: txt tab separated columns csv comma separated columns
#' @param logFC.threshold, minimal logFC present in at least one of the comparisons with respect to reference covariate
#' @param FDR.threshold, minimal FDR present in at least one of the comparisons with respect to reference covariate
#' @param logCPM.threshold, minimal average abundance
#' @param plot, TRUE if differentially expressed genes are represented in a plot.
#' @author Raffaele Calogero, raffaele.calogero [at] unito [dot] it, University of Torino, Italy
#'
#' @examples
#' \dontrun{
#' #running deDetection
#' system("wget http://130.192.119.59/public/buettner_counts_noSymb.txt.zip")
#' unzip("buettner_counts_noSymb.txt.zip")
#' lorenzFilter(group="docker", scratch.folder="/data/scratch/",
#' data.folder=getwd(), matrixName="buettner_counts_noSymb",
#' p_value=0.05, format="txt", separator='\t')
#'
#' system("wget ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/Mus_musculus.GRCm38.92.gtf.gz")
#' system("gzip -d Mus_musculus.GRCm38.92.gtf.gz")
#' scannobyGtf(group="docker", data.folder=getwd(),
#' counts.table="lorenz_buettner_counts_noSymb.txt",
#' gtf.name="Mus_musculus.GRCm38.92.gtf",
#' biotype="protein_coding", mt=FALSE, ribo.proteins=FALSE,
#' file.type="txt", umiXgene=3)
#'
#' deDetection(group="docker", data.folder=getwd(),
#' counts.table="annotated_lorenz_buettner_counts_noSymb.txt",
#' file.type="txt", logFC.threshold=1, FDR.threshold=0.05, logCPM.threshold=4, plot=TRUE)
#' }
#'
#' @export
deDetection <- function(group=c("sudo","docker"), data.folder, counts.table, file.type=c("txt","csv"), logFC.threshold=1, FDR.threshold, logCPM.threshold=4, plot=c(TRUE, FALSE)){
#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)
}
#storing the position of the home folder
home <- getwd()
setwd(data.folder)
#initialize status
system("echo 0 >& ExitStatusFile")
#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")
setwd(home)
return(10)
}
#executing the docker job
params <- paste("--cidfile ",data.folder,"/dockerID -v ", data.folder, ":/data -d docker.io/repbioinfo/desc.2018.01 Rscript /bin/desc.R ", counts.table, " ", file.type, sep="")
resultRun <- runDocker(group=group, params=params)
#waiting for the end of the container work
if(resultRun==0){
cat("\nDifferential expression analysis is finished\n")
}
tmp0 <- read.table(paste("DE_", counts.table, sep=""), sep="\t", header=T, row.names=1)
max0.logfc.tmp <- apply(tmp0[,grep("logFC", names(tmp0))], 1, function(x) unique(x[which(abs(x)== max(abs(x)))]))
max0.logfc <- sapply(max0.logfc.tmp, function(x)as.numeric(x[[1]]))
tmp <- tmp0[which(tmp0$logCPM >= logCPM.threshold),]
max.logfc <- apply(tmp[,grep("logFC", names(tmp))], 1, function(x) max(abs(x)))
tmp <- tmp[which(max.logfc >= logFC.threshold),]
tmp <- tmp[which(tmp$FDR <= FDR.threshold),]
max1.logfc.tmp <- apply(tmp[,grep("logFC", names(tmp))], 1, function(x){
x[which(abs(x)== max(abs(x)))]
})
max1.logfc <- sapply(max1.logfc.tmp, function(x)as.numeric(x[[1]]))
if(plot){
pdf("filteredDE.pdf")
plot(tmp0$logCPM, max0.logfc, xlab="log2CPM", ylab="log2FC", type="n")
points(tmp$logCPM, max1.logfc, pch=19, cex=0.5, col="red")
points(tmp0$logCPM, max0.logfc, pch=".", col="black")
abline(h=0, col="black", lty=2)
dev.off()
}
write.table(tmp, paste("filtered_DE_", counts.table, sep=""), sep="\t", col.names=NA)
#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("DE detection run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("DE detection system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("DE detection 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 folder
cat("\n\nRemoving the temporary file ....\n")
system("rm -fR dockerID")
system(paste("cp ",paste(path.package(package="rCASC"),"containers/containers.txt",sep="/")," ",data.folder, sep=""))
setwd(home)
}
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