循环遍历R中目录中的所有文件，应用多个命令 [英] Looping through all files in directory in R, applying multiple commands

问题描述

我需要在一个目录中的所有单个 .txt 文件（大约300）中应用一组命令。

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

我不太熟悉R，所以在线查看关于循环的所有帮助都是令人困惑的，或者我不能解决如何应用一个循环，当你需要应用多个命令每个文件

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.

我需要应用到目录中的每个文件（系统发育树）的命令（使用R的猿库）：

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")

如何应用一个将这些命令应用于每个单独的.txt文件（使用R或Unix命令行）？输出（例如unrootedtree123.txt）将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.

提前感谢
Dani。

Thanks in advance, Dani.

推荐答案

您可以获取所有文件，然后循环使用 lapply 并应用您想要的任何功能应用如下：

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

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