"TRUE" instead of "T" allele in R

Question

[manay]

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.

Answer 1

[Charles Plessy]

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_ !

[WouterDeCoster]

I would argue this is as bad as Excel converting gene names to dates.
I assume there is a better alternative to read.table() without these quirks?

[russhh]

Yes. Use readr and explicitly state the datatypes for the columns.

[Charles Plessy]

Not that I know,

> system("printf 'A C T G\nA C T G\n' > test.txt")
> read.table("test.txt")
  V1 V2   V3 V4
1  A  C TRUE  G
2  A  C TRUE  G

> data.table::fread("test.txt", head = F)
   V1 V2   V3 V4
1:  A  C TRUE  G
2:  A  C TRUE  G

> as.data.frame(readr::read_delim("test.txt", " ", col_names=FALSE))
Parsed with column specification:
cols(
  X1 = col_character(),
  X2 = col_character(),
  X3 = col_logical(),
  X4 = col_character()
)
  X1 X2   X3 X4
1  A  C TRUE  G
2  A  C TRUE  G

However, this only happens when a column only contains values that look like logical.

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

> read.table(text="A C T G\nA C F G\n")
  V1 V2    V3 V4
1  A  C  TRUE  G
2  A  C FALSE  G

> read.table(text="A C T G\nA C G G\n")
  V1 V2 V3 V4
1  A  C  T  G
2  A  C  G  G

[manay]

Thank you very much all of you !

colClasses="character" solved that problem.

[Charles Plessy]

You are welcome. Please click on the "Accept!" button so that my answer appears at the top of the list. This is important since the other answer does not solve the problem.

Answer 2

[Chris Miller]

I suspect that using "read.table( . . . stringAsFactors=F)" will solve your problem.

(edit - it will not! see the comprehensive answer above)