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rasmus.rydbirk
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@rasmusrydbirk-12534
Last seen 3.0 years ago
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!
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!