Question: "TRUE" instead of "T" allele in R
1
gravatar for manay
6 months ago by
manay10
manay10 wrote:

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.

R • 427 views
ADD COMMENTlink modified 6 months ago by Charles Plessy2.3k • written 6 months ago by manay10
6
gravatar for Charles Plessy
6 months ago by
Charles Plessy2.3k
Japan
Charles Plessy2.3k wrote:

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_ !

ADD COMMENTlink written 6 months ago by Charles Plessy2.3k

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?

ADD REPLYlink written 6 months ago by WouterDeCoster24k
2

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

ADD REPLYlink written 6 months ago by russhh2.8k
1

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
ADD REPLYlink written 6 months ago by Charles Plessy2.3k

Thank you very much all of you !

colClasses="character" solved that problem.

ADD REPLYlink written 6 months ago by manay10

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.

ADD REPLYlink written 6 months ago by Charles Plessy2.3k
2
gravatar for Chris Miller
6 months ago by
Chris Miller19k
Washington University in St. Louis, MO
Chris Miller19k wrote:

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

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

ADD COMMENTlink modified 5 months ago • written 6 months ago by Chris Miller19k
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