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Re: st: New program - snpgrab


From   Elwood Cook <danielecook@gmail.com>
To   statalist@hsphsun2.harvard.edu
Subject   Re: st: New program - snpgrab
Date   Mon, 30 Jan 2012 09:41:54 -0600

Regarding variable names: The program is intended as a data
retrieval/data management program. Ideally the user simply provides a
list of SNPs, and can pull in additional information using this ado
file.

-E

On Mon, Jan 30, 2012 at 9:32 AM, Nick Cox <njcoxstata@gmail.com> wrote:
> For this to work in Stata 10, the -version- statement would need to be
> changed and the line
>
> label define Chr_ID_lbl 23 "X" 24 "Y" 25 "MT", replace
>
> would need to be
>
> label define Chr_ID_lbl 23 "X" 24 "Y" 25 "MT", modify
>
> Nick
>
> On Mon, Jan 30, 2012 at 3:16 PM, Elwood Cook <danielecook@gmail.com> wrote:
>
>> Thanks for the feedback.
>>
>> (1.) This should be able to run under version 11.0, but I am not sure
>> about 10 as I am unable to test that.
>> (2.) I will create a help file in the next day or two.
>> (3.) The data is pulled in using the "efetch" utilities provided by
>> pubmed. (http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchseq_help.html)
>> (4.) Please feel free to provide more thoughts! If you'd like to try
>> it, you could type the following into Stata:
>>
>>
>>
>> set obs 100
>> gen snp = _n
>> snpgrab snp
>>
>>
>>
>> I will include more examples in the help file.
>>
>> I am also working on programs for pulling in data based on gene names,
>> ids and publication ID's.
>>
>> Thanks,
>> -E
>>
>> On Mon, Jan 30, 2012 at 5:30 AM, Tiago V. Pereira
>> <tiago.pereira@mbe.bio.br> wrote:
>>> I found the idea very interesting. However, I have some remarks:
>>>
>>> (1) it would be nice to change the version. For example,  version 12.0 to
>>> 10.0 (is that possible?)
>>> (2) Do you have a help file? I have failed to find it.
>>> (3) it is not clear for me where the data come from.
>>> (4) I have certainly more observations, but I would need to run it. I
>>> manually changed the original code to run -snpgrap- in my Stata 11.0 -
>>> unsuccessfully, however. An example would be very helpful.
>>>
>>> All the best,
>>>
>>> Tiago
>>>
>>>
>>>
>>> ----------------
>>> I have written a new program for those in the field of genetics.
>>>
>>> The program, called snpgrab, will download snp (single nucleotide
>>> polymorphism) information when provided with a list of rs numbers.
>>> This information includes Gene Name, Gene ID (Entrez), Chromosome,
>>> Position (bp), alleles, heterozygosity, and more.
>>>
>>> Please let me know what you think, and how this can be improved or
>>> expanded upon.You can install the program by typing in the following
>>> command:
>>>
>>>
>>> net install snpgrab, from(http://www.elwoodcook.com/stata/)
>>>
>>>
>>> To use, enter a list of snp numbers. They can be a string (with the rs
>>> prefix) or a numeric variable with the rs left out. Then type:
>>>
>>> snpgrab rslist
>>>
>>> where rslist is the variable of a list of snp numbers. (can be string,
>>> with rs prefix or numeric without).
>
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-- 
-E

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