Haploview: Unable to get an association plot from PLINK results

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10.0 years ago

prachimunjal14 ▴ 10

Dear All,

I am facing a problem in plotting PLINK (GWAS tool) generated association results using Haploview.

I am loading my data in Haploview and selecting X-axis (Chromosomes) and Y-axis (-log10 of P-value).

But an empty window of 'plot' is generated and disappears itself in 2 minutes.

Please help me with this.

Thanks a lot.

Haploview snp plot association-results • 4.2k views

ADD COMMENT • link updated 2.6 years ago by Ram 43k • written 10.0 years ago by prachimunjal14 ▴ 10

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Are you trying to make a Manhattan plot?

ADD REPLY • link 10.0 years ago by zx8754 11k

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Yes. Do you have any idea how to do that?

Thanks

ADD REPLY • link 10.0 years ago by prachimunjal14 ▴ 10

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This one is a bit old - Annotated Manhattan plots and QQ plots for GWAS using R - is a good start, also there are some R packages that will require data in specific format.

ADD REPLY • link updated 4.3 years ago by Ram 43k • written 9.9 years ago by zx8754 11k

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