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Re: st: New program - snpgrab


From   Nick Cox <njcoxstata@gmail.com>
To   statalist@hsphsun2.harvard.edu
Subject   Re: st: New program - snpgrab
Date   Mon, 30 Jan 2012 15:52:48 +0000

I trust that is an explanation for people working in the field.
Perhaps what such people do is start with an empty dataset and then
read in data and -snpgrab- uses more or less predictable names for
different variables.

It's not good practice in general that programs should make too many
presumptions about what names are, or are not, in use.

I imagine your help file will clarify these matters.

Nick

On Mon, Jan 30, 2012 at 3:41 PM, Elwood Cook <danielecook@gmail.com> wrote:
> 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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