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问题:
I am using R to calculate the mean values of a column in a file like so:
R file1 = read.table("x01") mean(file1$V4)
However I have no experience building loops involving R, only with bash. How would I convert this into a loop that did this for every file in a folder and saved the output into one file with the file name and mean value as the 2 columns for each row? eg:
x01(or file1 if that is simpler) 23.4 x02 25.4 x03 10.4
etc
(Don't mind if the solution is bash and R or exclusively R) Many thanks for your help!
Current error from one of the solutions using bash and R:
Error in `[.data.frame`(read.table("PercentWindowConservedRanked_Lowest_cleanfor1000genomes_1000regions_x013", : undefined columns selected Calls: mean -> [ -> [.data.frame Execution halted
回答1:
My solution is also similar to @jmsinger but you can specify the path to your files in the code itself and then calculate the mean like this :
filename <- system("ls /dir/",intern=TRUE) for(i in 1:length(filename)){ file <- read.table(filename[i],header=TRUE) ## if you have headers in your files ## mean <- mean(file$V4) write.table(mean,file=paste("/dir",paste("mean",filename[i],sep="."),sep="/")) ##if you wish to write the means of all the files in seperate files rather than one. }
hope this helps
回答2:
This is similar to what @jmsigner has done, but with minor changes. For instance, writing to a file is done at the end. The code has not been tested.
out <- lapply(list.files(), FUN = function(x) { m <- mean(read.table(x, header = TRUE)$V4) return(m) }) result <- do.call("cbind", out) #merge a list column-wise # before writing, you can make column names pretty with colnames() # e.g. colnames(result) <- c("x01", "x02") write.table(result, file = "means.txt")
回答3:
Assuming the columns are always named the same, you could do the following in R:
out.file <- 'means.txt' for (i in list.files()) { tmp.file <- read.table(i, header=TRUE) # Not sure if you have headers or not tmp.mean <- mean(tmp.file1$V4) write(paste0(i, "," tmp.mean), out.file, append=TRUE) }
Or the same thing with more bash:
for i in $(ls *) do mean=$(Rscript -e "mean(read.table('$i', header=T)[, 'V4'])") echo $i,$mean >> means.txt done
