Question: Allele Frequency correlation in R

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Cece •

**0**wrote: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

You tried this?

24k• written 3.7 years ago by Floris Brenk •890R matrices can be numeric, you'd need to post example data and code to get help for this.

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