Allele Frequency correlation in R

Question

[Cece]

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

[Floris Brenk]

You tried this?

data <- as.numeric(as.character(x))

[Ben]

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