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stephenturner / qqman

An R package for creating Q-Q and manhattan plots from GWAS results
http://cran.r-project.org/web/packages/qqman/
GNU General Public License v3.0
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strange Manhattan plots #14

Closed kkleinoros closed 10 years ago

kkleinoros commented 10 years ago

rplot

I am getting these strange Manhattan plots. I look at the hist of my pvalues they seem to be fine.

stephenturner commented 10 years ago

Please post some data as a github gist and put a link to your data here. Also drop in an image here so I can see what you're talking about.

kkleinoros commented 10 years ago

here is the link to the first 50 entries of my data https://gist.github.com/kt68

stephenturner commented 10 years ago

First off, the link showed only 10 lines of results. Second, if you'd like some help, best to include the data that's giving you the result that you're displaying above. When I plotted your data I'm not seeing any problem.

d <- read.table("test.txt", header=TRUE)
library(qqman)
manhattan(d)

rplot

kkleinoros commented 10 years ago

I have given you the same data. You are also getting points here instead of lines. Why is that?

From: Stephen Turner [mailto:notifications@github.com] Sent: Monday, June 23, 2014 12:43 PM To: stephenturner/qqman Cc: Kathleen Klein Subject: Re: [qqman] strange Manhattan plots (#14)

First off, the link showed only 10 lines of results. Second, if you'd like some help, best to include the data that's giving you the result that you're displaying above. When I plotted your data I'm not seeing any problem.

d <- read.table("test.txt", header=TRUE)

library(qqman)

manhattan(d)

[rplot]https://cloud.githubusercontent.com/assets/460076/3360687/76cb863e-faf5-11e3-8a42-e0439c44fc63.png

— Reply to this email directly or view it on GitHubhttps://github.com/stephenturner/qqman/issues/14#issuecomment-46869974.

stephenturner commented 10 years ago

I'm definitely not getting what you're getting. Post the rest of your data. This is what I get.

rplot01