读取目录中的所有文件并对每个数据框应用多个函数 [英] Read all files in directory and apply multiple functions to each data frame

问题描述

我需要将 R 中的一组命令应用于目录中的所有单个 .txt 文件(大约 300 个).

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

我对 R 不是很熟悉，所以我在网上看到的关于循环的所有帮助都令人困惑，或者当您需要对每个文件应用多个命令时，我无法弄清楚如何应用循环.

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.

我需要应用于目录中每个文件(系统发育树)的命令是(使用 R 的 ape 库):

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")

如何应用循环将这些命令应用到每个单独的 .txt 文件(使用 R 或在 Unix 命令行中)?输出(例如 unrootedtree123.txt)需要为每个单独的文件使用不同的名称.

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.

提前致谢，丹妮.

推荐答案

您可以获取所有文件，然后使用 lapply 循环并应用您想要应用的任何函数，如下所示:

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="	", quote=FALSE, row.names=FALSE, col.names=TRUE)
})

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