[R] read.table mystery

[David Winsemius]

On Mar 6, 2011, at 10:19 AM, Sarah Goslee wrote:

> 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.

There is also a fill argument for read.table that may be needed when  
the length of  colClasses or col.names exceeds the length of some rows.

-- 
David.
>
> 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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David Winsemius, MD
Heritage Laboratories
West Hartford, CT