How to loop over files in different directories

Question

I want to loop over multiple files and apply a function to them. The problem is that these files are all in different, but similarly named, directories. The pathway pattern is s

Answer 1

Have a look at ?list.files and ?dir, e.g.:

files <- list.files("/home/smith", pattern="Family[[:alnum:]]+.txt", recursive=TRUE, full.names=TRUE)

for (currentFile in files) {
  olddata <- read.table(currentFile, header=TRUE)
  ## some code
  write.table(newdata, file=sub(pattern=".txt$", replacement="test.txt", x=currentFile))
}

Or:

dirs <- dir("/home/smith", pattern="Family[[:alnum:]]+$")

fileName <- file.path(dirs, paste0(dirs, ".txt"))
testFileName <- file.path(dirs, paste0(dirs, "_test.txt"))

for (i in seq(along=fileName))

  olddata <- read.table(fileName[i], header=TRUE)
  ## some code
  write.table(newdata, file=testFileName[i])
}