Question: How to use qqman using own data?
gravatar for nbe
9 months ago by
nbe0 wrote:

I'm quite new to R so I installed the qqman package and everything and it says that the command to generate a Manhattan plot is the following:

manhattan(gwasResults, chr="CHR", bp="BP", snp="SNP", p="P" )

How can I replace their default data (gwasResults) with my own file and what type of file does it take? Is it an association file generated from PLINK?


R gwas • 639 views
ADD COMMENTlink written 9 months ago by nbe0

It is written in the first page of the manual: they are "Simulated GWAS results as obtained from plink --assoc." You can find the manual here

ADD REPLYlink written 9 months ago by Fabio Marroni2.4k
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