Write each element of a vector in file separated by tab - R

useraLlG 0
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I need to prepare a file for a tool I am using. The file should have the structure

Mutant
Mutant:A
Expression
Gene_A:0.5 Gene_B:1 Gene_C:3
Weight: 5

I wrote the following function to create such a file, where the value for the mutant and weight are used as inputs in the function, while the expression values (ie. Gene_A: 0.5 ... Gene_C:3) are taken from a vector. In the final file, I need the expression values to be separated by \t.

prep_file <- function(mutant, expression, weight, file_name){
  sink(paste0(file_name))
  cat("Mutant\n")
  cat(mutant,"\n")
  cat("Expression\n")
  cat(expression)
  cat("\n")
  cat("Weight:",weight)
  sink()
}

That can be used as such:

expres_vec <- c("Gene_A:0.5","Gene_B:1","Gene_C:3")
prep_file("Mutant:A",expres_vec,"5","test")

To create the test file in the example above.

How can I replace the cat(expression) in order to write each element of the expres_vec separated by a tab?

r
2 Answers

You can use the function paste with the collapse option. For example:

cat(paste(expres_vec, collpase = "\t"))

Where "\t" designates a tab (you can you any other character or regular expression here if needed).

Or in your function:

prep_file <- function(mutant, expression, weight, file_name){
  sink(paste0(file_name))
  cat("Mutant\n")
  cat(mutant,"\n")
  cat("Expression\n")
  cat(paste(expression, collpase = "\t"))
  cat("\n")
  cat("Weight:",weight)
  sink()
}
Thomas Guillerme0

You could list the arguments and name them with the formalArgs of the function, helpful especially if the output might get more lines i.e. arguments, in the future.

prep_file <- function(Mutant, Expression, Weight, file_name) {
  l <- list(mutant, expression, weight) |> setNames(paste0(formalArgs(prep_file)[1:3], ':'))
  invisible(Map(cat, lapply(names(l), paste0, '\n'), lapply(l, paste0, '\t'), '\n')) |>
    capture.output(file=file_name)
}

prep_file("Mutant:A", expres_vec, 5, "test")
# Mutant:
#   Mutant:A     
# Expression:
#   Gene_A:0.5   Gene_B:1    Gene_C:3    
# Weight:
#   5

Not sure, where the indentation comes from, but actually it improves readability :)

jay.sf0
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