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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 09:16:16 -0600

Hi,

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).
>
> Thanks,
> D. Elwood Cook
> *
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-- 
-E

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