read.table unexpectedly interprets "T" as TRUE

Question

I have found an issue where R seems to interpret "T" as TRUE even while using all means to avoid doing so (at least according to this post).

Example data (saved as "test.txt"):

col1    col2
1   T
2   T
3   T
4   T
5   T
6   T
7   T
8   T
9   T

Example code:

read.table("test.txt", as.is=TRUE, header=TRUE, 
   stringsAsFactors=FALSE, colClasses=c(character())) 

Produces:

  col1 col2
1    1 TRUE
2    2 TRUE
3    3 TRUE
4    4 TRUE
5    5 TRUE
6    6 TRUE
7    7 TRUE
8    8 TRUE
9    9 TRUE

Only non-ideal solution I found was to set header=FALSE:

read.table("test.txt", as.is=TRUE, header=FALSE, 
    stringsAsFactors=FALSE,
    colClasses=c(character()))        


     V1   V2
1  col1 col2
2     1    T
3     2    T
4     3    T
5     4    T
6     5    T
7     6    T
8     7    T
9     8    T
10    9    T

I realize this may seem somewhat contrived, but this edge case is genuine in that a human gene is named actually "T" (!) with values in col1 being positions within that gene.

Thanks in advance for the help

Answer 1

What makes you think this is "unexpectedly" ?

R guesses for you (and that is generally helpful), but if you know better, use the colClasses=... argument to tell R.

R> res <- read.table(textConnection("col1 col2\n1 T\n2 T\n3 T"), 
+                    header=TRUE, colClasses=c("numeric", "character"))
R> res
    col1 col2
 1    1    T 
 2    2    T 
 3    3    T 
R> sapply(res, class)
        col1        col2  
   "numeric" "character"  
R>

Your post was a little oddly formatted so I didn't see at first that you did in fact specify colClasses. Despite the recycling rule I always recommend to supply a vector with as many entries as you have columns.