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Question: Manhattan plot from ChAMP data
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gravatar for rasmus.rydbirk
18 months ago by
rasmus.rydbirk • 10
rasmus.rydbirk • 10 wrote:

I'm really confused as to why a function to create a Manhattan plot is not included in ChAMP. However, as a novice user of ChAMP I have troubles extraction data on probes/chromosome (frequency) and chrosome size which I assume is including in the software somewhere.

Can somebody help me locate this information? I'm using the EPIC platform. Thank you in advance!
champ plot manhattan plot
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modified 18 months ago by Yuan Tian • 80 • written 18 months ago by rasmus.rydbirk • 10
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gravatar for Yuan Tian
18 months ago by
Yuan Tian • 80
London
Yuan Tian • 80 wrote:
Hello: Sorry for not including Manhattan plot in it, maybe you can send me a link of paper indicating applying Manhatton plot for DNA methylation data, then I will consider included it in next version package. Also, what data exactly you want to extract from ChAMP? what is chromosome size? ChAMP indeed included some annotations, they are located in pacakge ChAMPdata. You may check the manual there to see all annotation included. Best
ADD COMMENT • link modified 18 months ago • written 18 months ago by Yuan Tian • 80

Thank you for the reply.

As I understand it, Manhattan plots can be made using beta value ranges (example: http://dx.doi.org/10.1007/s12017-014-8332-8) or simply -log10(p) (https://en.wikipedia.org/wiki/Manhattan_plot). Beta values are already available after champ.impute (or before if impute is not performed), so that's easy. p-values can be derived at different steps in ChAMP, it can be DMP data or it can be post champ.process: If a simple setup is made where it is easy to import p-values calculated after ChAMP processing, that would probably be the easiest/best method.

The QQman package has a good description of creating Manhattan plots:

http://www.gettinggeneticsdone.com/2014/05/qqman-r-package-for-qq-and-manhattan-plots-for-gwas-results.html

For now I will look closer into the ChAMPdata and the manual. Thank you!

ADD REPLY • link written 18 months ago by rasmus.rydbirk • 10
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