Plots using GWAS and eQTL datasets with locuszoom
Does anyone know how to include two datasets in locuszoom ? Something like this? On the locuszoom documentation for the standalone program, it doesn't really tell you how to go about two datasets. The command I am trying to use is
locuszoom \
--metal file fineMap=GWASeQTL\
--markercol SNP \
--pvalcol P \
--delim tab \
--refgene Gene1 \
--flank 500kb \
--pop EUR \
--build hg19 \
--source 1000G_March2012
where, file looks like this
SNP P
SNP1 0.1
SNP1 0.3
SNP2 0.2
SNP3 0.25
and GWASeQTL looks like this
snp chr pos pp group color
SNP1 1 1000 0.1 eQTL red
SNP1 1 1000 0.3 GWAS blue
SNP2 12 1153 0.2 eQTL red
Anyone does this before?
1 answer
I think for Figure 2 in the paper you linked, it cannot be done by LocusZoom. The author did not do that, obviously.
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Phoenix Mu •
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