[R] Fwd: read.table() and scientific notation

[Alex Brown]

note: this e-mail is supposed to precede my coerce hack one.

As an example of the other posters mentioning colClasses, with some  
debugging notes:

# create a pretend file for this example

 > Lines <- scan(sep="\n", what="")
a 1 3e-8
b 2 1e+10
c 3 e-10
d 4 e+3

 > file <- textConnection(Lines)

# import as you would a file, and specify the column types.
 > T <- read.table(file, colClasses=list("character", "integer",  
"double"))
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,  
na.strings,  :
	scan() expected 'a real', got 'e-10'

# decide that's not very helpful.  let's just import everything as  
character:
# restarting the file.
 >file <- textConnection(Lines)
 >T <- read.table(file, colClasses="character")
 >lapply(T, mode)
$V1
[1] "character"

$V2
[1] "character"

$V3
[1] "character"


 > T
   V1 V2    V3
1  a  1  3e-8
2  b  2 1e+10
3  c  3  e-10
4  d  4   e+3

# try the conversion to double:

 > (D<-as.double(T$V3))
[1] 3e-08 1e+10    NA    NA
Warning message:
NAs introduced by coercion

# let's see which are bad:
 > T[is.na(D),]
   V1 V2   V3
3  c  3 e-10
4  d  4  e+3



-Alex



On 10 Oct 2006, at 12:17, January Weiner wrote:

> Oh, thanks, that was hint enough :-) I see it now. I turns that R does
> not understand
>
> e-10
>
> ...which stands for 1e-10 and is produced by some of the bioinformatic
> applications that I use (notably BLAST). However, R instead of being
> verbose on that just assumes that the whole column is a string.
>
> Is there a way to enforce a specific conversion in R (for example, to
> be able to see where the errors are?).
>
> January
>
> -- 
> ------------ January Weiner 3  ---------------------+---------------
> Division of Bioinformatics, University of Muenster  |  Schloßplatz 4
> (+49)(251)8321634                                   |  D48149 Münster
> http://www.uni-muenster.de/Biologie.Botanik/ebb/    |  Germany
>
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