Question

The problem

I have a tab delimited input file that looks like so:

Variable [1]    Variable [2]
111    Something
Nothing    222

The first row represents column names and the two next rows represents column values. As you can see, the column names includes both spaces and some tricky signs.

Now, what I want to do is to import this file into R and then output it again to a new text file, making it look exactly the same as the input. For this purpose I have created the following script (assuming that the input file is called “Test.txt”):

file <- "Test.txt"
x <- read.table(file, header = TRUE, sep = "\t")
write.table(x, file = "TestOutput.txt", sep = "\t", col.names = TRUE, row.names = FALSE)

From this, I get an output that looks like this:

"Variable..1."  "Variable..2."
"1"    "111"    "Something"
"2"    "Nothing"    "222"

Now, there are a couple of problems with this output.

1. The “[” and “]” signs have been converted to dots.
2. The spaces have been converted to dots.
3. Quote signs have appeared everywhere.

How can I make the output file look exactly the same as the input file?

What I’ve tried so far

Regarding problem number one and two, I’ve tried specifying the column names through creating an internal vector, c("Variable [1]", "Variable [2]"), and then using the col.names option for read.table(). This gives me the exact same output. I’ve also tried different encodings, through the encoding option for table.read(). If I look at the internally created vector, mentioned above, it prints the variable names as they should be printed so I guess there is a problem with the conversion between the “text -> R” and the “R -> text” phases of the process. That is, if I look at the data frame created by read.table() without any internally created vectors, the column names are wrong.

As for problem number three, I’m pretty much lost and haven’t been able to figure out what I should try.

Answer 1

Given the following input file as test.txt:

Variable [1]    Variable [2]
111 Something
Nothing 222

Where the columns are tab-separated you can use the following code to create an exact copy:

a <- read.table(file='test.txt', check.names=F, sep='\t', header=T, 
    stringsAsFactors=F)
write.table(x=a, file='test_copy.txt', quote=F, row.names=F, 
    col.names=T, sep='\t')