#' @title A function allowing the identification of differentially expressed genes if multiple groups are provided.
#' @description This function executes in a docker edgeR for the identification of differentially expressed genes in bulk RNAseq. IMPORTANT the filename shoould not have any '.' in the name unless .txt
#' @param group, a character string. Two options: sudo or docker, depending to which group the user belongs
#' @param file, a character string indicating the path of the file, with counts.table name and extension included
#' @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
#' anovaLike(group="docker", file=paste(getwd(),"annotated_lorenz_buettner_counts_noSymb.txt", sep="/"),
#' logFC.threshold=1, FDR.threshold=0.05, logCPM.threshold=4)
#' }
#'
#' @export
anovaLike <- function(group=c("sudo","docker"), file, logFC.threshold=1, FDR.threshold, logCPM.threshold=4, plot=c(TRUE, FALSE)){
data.folder=dirname(file)
positions=length(strsplit(basename(file),"\\.")[[1]])
matrixNameC=strsplit(basename(file),"\\.")[[1]]
matrixName=paste(matrixNameC[seq(1,positions-1)],collapse="")
format=strsplit(basename(basename(file)),"\\.")[[1]][positions]
file.type=format
counts.table=paste(matrixName, file.type, sep=".")
#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.2018.02 Rscript /bin/debulk.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")
}
system(paste("mv DE_", counts.table, " ANOVAlike_", counts.table, sep=""))
tmp0 <- read.table(paste("ANOVAlike_", counts.table, sep=""), sep="\t", header=T, row.names=1)
tmp0.names <- rownames(tmp0)
tmp0.names1 <- strsplit(tmp0.names, ":")
tmp0.names2 <- sapply(tmp0.names1, function(x)x[1])
zz <- file("bkg2GO.txt", "w")
writeLines(tmp0.names2, con=zz)
close(zz)
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("filtered_ANOVAlike.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_ANOVAlike_", counts.table, sep=""), sep="\t", col.names=NA)
tmp.names <- rownames(tmp)
tmp.names1 <- strsplit(tmp.names, ":")
tmp.names2 <- sapply(tmp.names1, function(x)x[1])
zz <- file("genesGO.txt", "w")
writeLines(tmp.names2, con=zz)
close(zz)
#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("Anova-like user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("Anova-like system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("Anova-like elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}else{
tmp.run <- NULL
tmp.run[1] <- paste("Anova-like run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("Anova-like system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("Anova-like 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="docker4seq"),"containers/containers.txt",sep="/")," ",data.folder, sep=""))
setwd(home)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.