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Re: st: Manhattan Plots in Stata (Genetics)


From   Nick Cox <njcoxstata@gmail.com>
To   statalist@hsphsun2.harvard.edu
Subject   Re: st: Manhattan Plots in Stata (Genetics)
Date   Thu, 22 Sep 2011 18:08:42 +0100

Don't worry too much about any of that.

An example can be trivial and be based on fake data. SSC and SJ both
support the distribution of ancillary files as appropriate. It's the
user's concern to find interesting data. The point about the help file
is that correct examples are clearer and cut down on the user
enquiries you may well receive.

Nick

On Thu, Sep 22, 2011 at 5:43 PM, Cook, Daniel E <daniel-e-cook@uiowa.edu> wrote:
> I should also note that I haven't created any examples because I do not have a GWAS dataset that I am allowed to distribute. I can create dummy GWAS data but I have yet to figure out how to do so.
>
> -E
>
> -----Original Message-----
> From: owner-statalist@hsphsun2.harvard.edu [mailto:owner-statalist@hsphsun2.harvard.edu] On Behalf Of Nick Cox
> Sent: Thursday, September 22, 2011 11:02 AM
> To: statalist@hsphsun2.harvard.edu
> Subject: Re: st: Manhattan Plots in Stata (Genetics)
>
> Please note the preference on Statalist for use of real-name identifiers.
>
> As Phil Schumm notes, this is a key area for many Stata users.
>
> Various quick suggestions:
>
> 1. A detail in -manhattan- is your use of -egen- to generate new variables which are for holding single scalars that are e.g. minimum, maximum, or total. This is unnecessary and indeed inefficient when -summarize, meanonly- can be used for that purpose (including calculation of totals).
>
> 2. There is no support for -if- or -in- restrictions.
>
> 3. The help file should include an email address for support and examples that will run. The variable name "P-values" is illegal, so the example won't run.
>
> 4. Your style is your own, but predominant Stata style for messages is more neutral than yours.
>
> Nick
>
> On Thu, Sep 22, 2011 at 4:16 PM, irishcocacola <daniel-e-cook@uiowa.edu> wrote:
>> Anyone out there using Stata for genome wide association studies
>> (GWAS)? Do you have an interest in an ado file program that allows you
>> to create manhattan plots in Stata?
>>
>> I have written one and would like to distribute it and get feedback.
>>
>> You can install using this (it also includes a help file).
>> net install http://www.thestringery.com/elwoodcook/manhattan.pkg
>>

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