Question: Plots using GWAS and eQTL datasets with locuszoom
gravatar for Nandini
5.5 years ago by
Nandini840 wrote:

Does anyone know how to include two datasets in locuszoom ? Something like this  Plots ? On the locuzoom 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

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?


locuszoom plots gwas and eqtl • 2.1k views
ADD COMMENTlink modified 13 months ago by Phoenix Mu20 • written 5.5 years ago by Nandini840
gravatar for Phoenix Mu
13 months ago by
Phoenix Mu20
Phoenix Mu20 wrote:

I think for Figure 2 in the paper you linked, it cannot be done by LocusZoom. The author did not do that, obviously.

ADD COMMENTlink written 13 months ago by Phoenix Mu20
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