Question: Allele Frequency correlation in R
0
gravatar for Cece
3.2 years ago by
Cece0
United States/Houston
Cece0 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

myposts • 1.3k views
ADD COMMENTlink written 3.2 years ago by Cece0

You tried this?

data <- as.numeric(as.character(x))
ADD REPLYlink modified 7 months ago by RamRS21k • written 3.2 years ago by Floris Brenk890

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

ADD REPLYlink written 3.2 years ago by Ben2.0k
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