How do you make a Manhattan plot that is zoomed in on a single chromosome?

Questions about GenABEL (aka *ABEL) suite of packages
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Erin.Davis
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Joined: Mon Feb 01, 2016 8:21 pm

How do you make a Manhattan plot that is zoomed in on a single chromosome?

Postby Erin.Davis » Mon Feb 01, 2016 9:43 pm

I am analyzing SNP chip data from horses using the GenABLE package. I have been able to run the quality control and association tests as well as make a Manhattan plot of all the chromosomes. I now want to use the same association test and look at individual chromosomes. I have not been able to find a way to subset one chromosome from the data after the quality control and association tests have been run. Is there a way to do this? Does anyone know how?

Thank you

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