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

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.

Answer 1

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)
})