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RE: st: Manhattan Plots in Stata (Genetics)


From   "Cook, Daniel E" <daniel-e-cook@uiowa.edu>
To   "statalist@hsphsun2.harvard.edu" <statalist@hsphsun2.harvard.edu>
Subject   RE: st: Manhattan Plots in Stata (Genetics)
Date   Thu, 22 Sep 2011 16:43:24 +0000

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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