Hi,

I have a data set which includes A, T,C,G. 
When I use read.table command for this data set, I see TRUE's in terms of T alleles. It happens if the entire column just includes T. How can I fix that problem?

Thanks.

`read.table()` tries to guess the class of the input data and will sometimes be mislead.

    > read.table(text=("A C G T"))
      V1 V2 V3   V4
    1  A  C  G TRUE

    > summary(read.table(text=("A C G T")))
     V1    V2    V3       V4         
     A:1   C:1   G:1   Mode:logical  
                       TRUE:1        
                       NA's:0 

It is possible to specify in advance the class of the columns; see `?read.table` for details.

    > read.table(text=("A C G T"), colClasses = "character")
      V1 V2 V3 V4
    1  A  C  G  T

Related to Chris's answer in this particular case, `stringAsFactors` will not solve the problem.

    > read.table(text=("A C G T"), stringsAsFactors = FALSE)
      V1 V2 V3   V4
    1  A  C  G TRUE

Note that there are other cases where `T` may be coerced to `TRUE` instead of `"T"`.  In particular, pay attention that [there is one gene whose symbol is _T_](https://en.wikipedia.org/wiki/Brachyury) !