Read all files in directory and apply multiple functions to each data frame

Question

I need to apply a set of commands in R to all the individual .txt files (around 300) in a directory.

I'm not very familiar with R, so all the help I've looked at online about looping is confusing, or I can't work out how to apply a loop when you need to apply multiple commands to each file.

The commands I need to apply to each file (phylogenetic trees) within the directory are (which uses R's ape library):

testtree <- read.tree("tree123.txt")
unrooted_tr <- unroot(testtree)
write.tree(unrooted_tr, file="unrootedtree123.txt")

How do I apply a loop which will apply these commands to each individual .txt file (either using R or in the Unix command line)? The output (e.g. unrootedtree123.txt) will need to have a different name for each individual file.

Thanks in advance, Dani.

Solution

You can get all the files and then loop using lapply and apply whatever function you want to apply as follows:

files <- list.files(path="path/to/dir", pattern="*.txt", full.names=TRUE, recursive=FALSE)
lapply(files, function(x) {
    t <- read.table(x, header=TRUE) # load file
    # apply function
    out <- function(t)
    # write to file
    write.table(out, "path/to/output", sep="\t", quote=FALSE, row.names=FALSE, col.names=TRUE)
})

Comments

[muad]

This does not work. Looping through a directory of csvs gives this error: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 2 elements