Re: [R] read.table mystery

From: Sarah Goslee <sarah.goslee_at_gmail.com>
Date: Sun, 06 Mar 2011 10:19:04 -0500

Not so much a mystery. read.table() only looks at the first 5 lines when decided how many columns your file has (as described in the Details section of the help).

The easiest solution is to add a col.names argument to read.table() with the correct number of names.

You may want to also include as.is=TRUE if you don't want your data to be imported as factors. If you expect character but have factor you may get unexpected results later.

Sarah

On Sun, Mar 6, 2011 at 5:04 AM, Johannes Graumann <johannes_graumann_at_web.de> wrote:
> Hello,
>
> Please have a look at the code below, which I use to read in the attached
> file. As line 18 of the file reads "1065:>sp|Q9V3T9|ADRO_DROME
> NADPH:adrenodoxin oxidoreductase, mitochondrial OS=Drosophila melanogaster
> GN=dare PE=2 SV=1", I expect the code below to produce a 3 column data frame
> with most of the last column empty and line 18 to produce a data.frame row
> like so:
>
> V1
> 1065
> V2
> >sp|Q9V3T9|ADRO_DROME NADPH
> V3
> adrenodoxin oxidoreductase, mitochondrial OS=Drosophila
> melanogaster GN=dare PE=2 SV=1
>
> Why is that not so?
>
> Thanks for any hint.
>
> Sincerely, Joh
>
> read.table(
> "/tmp/testfile.txt",
> sep=":",
> header=FALSE,
> quote="",
> fill=TRUE
> )[19,]

---
Sarah Goslee
http://www.functionaldiversity.org

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