R - Files not found when call to import folder, but open as individual files and list.files shows all?

问题

I have a bit of code used successfully before. It should import all files in a given directory into a single dataset. I have a new folder of data, and now I can't get it to work. The individual files will read in. List.files will also show all files in the folder. So I'm at a loss.

list.files('../data/')
[1] "B101-2.txt" "B101.txt"   "B116.txt"   "B6.txt"     "B65.txt"    "B67-2.txt"  "B67.txt"   
[8] "B70.txt"    "B71-2.txt"  "B71.txt"    "B95-2.txt"  "B95.txt"    "B96-2.txt"  "B96.txt"   
[15] "B98-2.txt"  "B98.txt"    "B99-2.txt"  "B99.txt"   

a = ldply(
.data = list.files(
    path = '../data/'
        )
, .fun = function(x){
    from_header = scan(x,n = 1,skip=1,quiet=T)
    to_return = read.table(
        file = x
        , skip = 20
        , sep = '\t'
        , fill = TRUE
            )
    to_return$condition = from_header[1]
    return(to_return)
        }
, .progress = 'text'
)

Error in file(file, "r") : cannot open the connection In addition: Warning message: In file(file, "r") : cannot open file 'B101-2.txt': No such file or directory

回答1:

Specifying the full path name can be done in list.files directly.

list.files(path = '../data', full.names = TRUE)

Note the omission of / in the path specification. If left in, the files would be listed as ..data//B101-2.txt, which would fail.

TEST Simulating a file structure you note in Tim Biegeleisen's answer:

library(plyr)
dir.create("analysis")
dir.create("data")
write.table(matrix(c(1:57,1:6), ncol=3, byrow=T), file="data/test1.txt", sep="\t", row.names=F, quote=F)
write.table(matrix(c(2:58,7:12), ncol=3, byrow=T), file="data/test2.txt", sep="\t", row.names=F, quote=F)
write.table(matrix(c(3:59,13:18), ncol=3, byrow=T), file="data/test3.txt", sep="\t", row.names=F, quote=F)

We now run your code from within the analysis folder.

setwd("analysis")
a = ldply(
.data = list.files(path = '../data', full.names = TRUE)
, .fun = function(x){
    from_header = scan(x,n = 1,skip=1,quiet=T)
    to_return = read.table(file = x, skip = 20, sep = '\t', fill = TRUE)
    to_return$condition = from_header[1]
    return(to_return)
        }
, .progress = 'text'
)

The code reads in all three files and outputs lines 21-22 for each.

a
  V1 V2 V3 condition
1  1  2  3         1
2  4  5  6         1
3  7  8  9         2
4 10 11 12         2
5 13 14 15         3
6 16 17 18         3

回答2:

list.files('../data/') is showing you output like B101-2.txt etc. for the files, but from your very call to list.files() you can see that the relative path is ../data/. So if you were to try to do, for example, read.csv(file="B101-2.txt") it would fail. Instead, the call should be read.csv(file="../data/B101-2.txt"). The solution to your problem is to use the full relative path necessary to address the files.

Use this as the first argument to ldply():

.data = paste0("../data/", list.files(path = '../data/'))

The key thing to take away from this is that list.files() returns a list of filenames (with extensions), not the full or relative path to those files.

来源：https://stackoverflow.com/questions/38006597/r-files-not-found-when-call-to-import-folder-but-open-as-individual-files-and

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