Renaming dataframes in R after read in via loop

Question

I'm trying to read in a bunch of .tsv files from a folder ('Test'), and I got this far:

files <- list.files("Test", pattern="*.tsv", full.names=TRUE)

for (i in 1:length(files)) assign(files[i], read.delim(files[i], na.strings = c(
"FAILED", "ERROR"))
)

This works, however the data frames it creates includes the file path and extension (in this case Test/ and .tsv resulting in a data frame named Test/100_1.tsv). I've been playing around with the code for a few hours trying to get it to name each data frame by the necessary information only (e.g., 100_1). If anyone has any suggestions, this novice would greatly appreciate the help.

create a new variable for the assign function like fnames <- sub(".*(?<=\\/)(.*)(?=\\.tsv).*", "\\1", files, perl=T) — Pierre L
– Pierre L, Commented Sep 15, 2015 at 17:13

user295691 · Accepted Answer · 2015-09-15 17:19:46Z

1

I would suggest loading these as a list, rather than into the global namespace with assign.

Something like

files <- list.files("Test", pattern="*.tsv", full.names=TRUE)
names(files) <- files
all.data <- lapply(files, function(fle) {
  read.delim(fle, na.strings=c("FAILED", "ERROR"))
})

will yield a list keyed by filename, which will be much easier to deal with.

answered Sep 15, 2015 at 17:19

user295691

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Badger · Accepted Answer · 2015-09-15 17:11:45Z

0

I would make a label object that contains the names you would like to apply to your dataframes. The label object I made assumes you always have the same size names. Should do what you are looking for though.

files <- list.files("Test", pattern="*.tsv", full.names=TRUE)
dflabels <- substr(files,5,nchar(files)-4)

for (i in 1:length(files)) assign(dflabels[i], read.delim(files[i], na.strings = c(
"FAILED", "ERROR"))
)

answered Sep 15, 2015 at 17:11

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rer · Accepted Answer · 2015-09-15 17:22:09Z

0

If you're just trying to get 100_1.tsv all you need to do is set full.names = FALSE and preset your working directory rather than call it in list.files.

E.g.

setwd("C:/Your/Working/Directory/Test")    
files <- list.files(pattern="*.tsv")
for (i in 1:length(files)) assign(files[i], read.delim(files[i], na.strings = c(
"FAILED", "ERROR"))
)

full.names defaults to FALSE.

edited Sep 15, 2015 at 17:22

answered Sep 15, 2015 at 17:15

rer

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