[R] R eat my data

[Shi, Tao]

Changbin,

It looks you're trying to read in a gene annotation file and usually it has many strange characters, e.g. "#", "&", ....  (as other people also suggest).   I encounter this all the time.  So try to be very thorough about your search (the first place I'll look for is the line where R stop reading.  See if any thing strange there.)  

Also, changing "read.table" to "read.delim" often works.

...Tao





----- Original Message ----
> From: Changbin Du <changbind at gmail.com>
> To: David Winsemius <dwinsemius at comcast.net>
> Cc: r-help at r-project.org
> Sent: Tue, May 25, 2010 9:12:58 AM
> Subject: Re: [R] R eat my data
> 
> 644727344    ABC-2 type transporter    ABC-2 type 
> transporter
644727345    conserved hypothetical protein  
>   conserved hypothetical
protein

Here is the last two lines of 
> the file id_name_gh5.txt.



On Tue, May 25, 2010 at 8:57 AM, David 
> Winsemius <
> href="mailto:dwinsemius at comcast.net">dwinsemius at comcast.net>wrote:

>
> 
> On May 25, 2010, at 11:42 AM, Changbin Du wrote:
>
>  HI, Dear 
> R community,
>>
>> My original file has 1932 lines, but when I 
> read into R, it changed to
>> 1068
>> lines, how 
> comes?
>>
>
> We are being asked to investigate this quest, 
> how?
>
> Have you looked at the last line to see if it looks like 
> gene_name?
>
> Isn't this isomorphic to genetics questions? What 
> sort of mutation is it?
> Deletion? Abnormal stop codon? Figure out where 
> the transcription process
> went wrong.  This sort of analysis would 
> appear to be right up the alley of
> someone doing 
> genetics.
>
>
>
>>
>> cdu at nuuk:~/operon$ wc 
> -l id_name_gh5.txt
>> 1932 
> id_name_gh5.txt
>>
>>
>>  
> gene_name<-read.table("/home/cdu/operon/id_name_gh5.txt", 
> sep="\t",
>>>
>> skip=0, header=F, 
> fill=T)
>>
>>> dim(gene_name)
>>>
>> 
> [1] 1068    3
>>
>>
>> 
> --
>>
>
>
> David Winsemius, MD
> West 
> Hartford, CT
>
>


-- 
> 
Sincerely,
Changbin
--

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