manhattan plot with vcf information
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10 weeks ago
sooni ▴ 10

Hello.

I imported the VCF file and combined FIX and INFO to create a data frame. This data frame contains VCF file information such as CHROM, POS, REF, ALT, QUAL, FILTER, etc. I want to draw a manhattan plot with this data frame. The problem is that p-value is needed to draw the manhattan plot. With this information I have, how can I find the p-value and draw a manhattan plot?

enter image description here

The image above is an image that only retrieves the CHROM, POS, REF, ALT, and QUAL information for the data frame I have.

How can I find the p-value and get the manhattan plot?

Please help me.

Thank you.

R manhattan vcf • 572 views
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The SNP data is only one part of the input for GWAS analyses, you also need phenotype data, then you can calculate GWAS stats which will include the p values.

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I don't know much about GWAS, so what kind of data is an example of phenotype data? Is it something like gender?

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I made the assumption you wanted a GWAS since that is the most common analysis represented in a manhattan plot. What analysis are you looking to plot in the manhattan plot?

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I want to find out specific genes using the manhattan plot. I divide the patients into two groups, controls and patients, and try to identify specific genes that differ in expression between the two groups. The picture below is the type of picture I want to do.

enter image description here

The figure is taken from the paper by Ji-Hye Oh et.al, 2023.

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Manhattan plots aren't typically used in DEG analyses. I suspect you're after a volcano plot. Hard to say from the picture alone, but that looks like a GWAS study, not a DEG one.

Also, just a minor point, but plots are simply used to represent and highlight data. The analyses you conduct are what identifies outliers.

From what I've gleaned about the data you have, you should be looking at differential expression studies.

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