CODEWITHSUNDEEP
rloopsfilenames
dede
dede

Reputation: 1171

For loop with file names in R

I have a list of files like:

nE_pT_sbj01_e2_2.csv, nE_pT_sbj02_e2_2.csv, nE_pT_sbj04_e2_2.csv, nE_pT_sbj05_e2_2.csv, nE_pT_sbj09_e2_2.csv, nE_pT_sbj10_e2_2.csv

As you can see, the name of the files is the same with the exception of 'sbj' (the number of the subject) which is not consecutive.

I need to run a for loop, but I would like to retain the original number of the subject. How to do this? I assume I need to replace length(file) with something that keeps the original number of the subject, but not sure how to do it.

setwd("/path")

file = list.files(pattern="\\.csv$") 
for(i in 1:length(file)){
  data=read.table(file[i],header=TRUE,sep=",",row.names=NULL)
  source("functionE.R")
  Output = paste("e_sbj", i, "_e2.Rdata")
  save.image(Output)
}

The code above gives me as output:

e_sbj1_e2.Rdata,e_sbj2_e2.Rdata,e_sbj3_e2.Rdata, e_sbj4_e2.Rdata,e_sbj5_e2.Rdata,e_sbj6_e2.Rdata.

Instead, I would like to obtain:

e_sbj01_e2.Rdata,e_sbj02_e2.Rdata,e_sbj04_e2.Rdata, e_sbj05_e2.Rdata,e_sbj09_e2.Rdata,e_sbj10_e2.Rdata.

Upvotes: 4

Views: 11641

Answers (3)

zx8754
zx8754

Reputation: 56004

Drop the extension "csv", then add "Rdata", and use filenames in the loop, for example:

myFiles <- list.files(pattern = "\\.csv$") 

for(i in myFiles){
  myDf <- read.csv(i)
  outputFile <- paste0(tools::file_path_sans_ext(i), ".Rdata")
  outputFile <- gsub("nE_pT_", "e_", outputFile, fixed = TRUE)
  save(myDf, file = outputFile)
}

Note: I changed your variable names, try to avoid using function names as a variable name.

Upvotes: 4

Łukasz Deryło
Łukasz Deryło

Reputation: 1860

If I understood correctly, you only change extension from .csv to .Rdata, remove last "_2" and change prefix from "nE_pT" to "e". If yes, this should work:

Output = sub("_2.csv", ".Rdata", sub("nE_pT, "e", file[i]))

Upvotes: 1

Val
Val

Reputation: 7023

If you use regular expressions and sprintf (or paste0), you can do it easily without a loop:

fls <- c('nE_pT_sbj01_e2_2.csv', 'nE_pT_sbj02_e2_2.csv', 'nE_pT_sbj04_e2_2.csv', 'nE_pT_sbj05_e2_2.csv', 'nE_pT_sbj09_e2_2.csv', 'nE_pT_sbj10_e2_2.csv')


sprintf('e_%s_e2.Rdata',regmatches(fls,regexpr('sbj\\d{2}',fls)))

[1] "e_sbj01_e2.Rdata" "e_sbj02_e2.Rdata" "e_sbj04_e2.Rdata" "e_sbj05_e2.Rdata" "e_sbj09_e2.Rdata" "e_sbj10_e2.Rdata"

You can easily feed the vector to a function (if possible) or feed the function to the vector with sapply or lapply

fls_new <- sprintf('e_%s_e2.Rdata',regmatches(fls,regexpr('sbj\\d{2}',fls)))

res <- lapply(fls_new,function(x) yourfunction(x))

Upvotes: 1

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