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 > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.