Manhattan plot from ChAMP data

Answer: Manhattan plot from ChAMP data

2.6 years ago by

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 2.6 years ago • written 2.6 years 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 2.6 years ago by rasmus.rydbirk • 10

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