RE: st: Manhattan Plots in Stata (Genetics)

["Cook, Daniel E" <daniel-e-cook@uiowa.edu>]

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
>
*
*   For searches and help try:
*   http://www.stata.com/help.cgi?search
*   http://www.stata.com/support/statalist/faq
*   http://www.ats.ucla.edu/stat/stata/


________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
________________________________

*
*   For searches and help try:
*   http://www.stata.com/help.cgi?search
*   http://www.stata.com/support/statalist/faq
*   http://www.ats.ucla.edu/stat/stata/