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Allele Frequency correlation in R

Hi,

I'm trying to run a correlation of allele frequencies of my two populations. My datasets are from plink so I imported them into R with read.plink. Problem is, R says they're matrices. I was trying to use cor.test but data has to be numeric. I tried to transform them to numeric using as.data.frame(x) but the transformation just hangs and doesn't complete. Can anyone advise how I can get this done? I'm trying to look at the frequencies as a way of assessing any batch effect.

Thanks,
Cece

plink r
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updated by Ram Ram • written by Cece • Cece

You tried this?

data <- as.numeric(as.character(x))
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updated by Ram Ram • written by Floris Brenk Floris Brenk

R matrices can be numeric, you'd need to post example data and code to get help for this.

• 1 views • link
written by Ben Ben

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