Question: Calculating Kappa value between two SNP matrices in R
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gravatar for elite420
16 months ago by
elite4200
elite4200 wrote:

Hi,

I have a problem calculating the kappa value between two SNPMatrices in R. I've made two SNP Matrices (in 'values' section in global environment) in R using 2 ped files of 27 individual's 810,000 SNP data.

(each ped file contains 27 rows which represent each individuals and 810,000 columns which represent SNP datas(the alleles) and 27 individuals in each ped file are the same individuals. But I,m trying to calculate the Kappa value between those two files because 810000 SNP data of the individuals may have differed since there are time difference between the two datas)

I used irr package to calculate the kappa value between two SNP matrices.

irr::kappa2(cbind(matrix(q), matrix(w)))

In the above code, 'q' and 'w' are the two SNP Matrices. But an error occurs.

Error in order(y) : unimplemented type 'raw' in 'orderVector1'

How can I fix this problem? Or is there another way to calculate the kappa value between the two SNPMatrices?

R ped snp gwas kappa • 287 views
ADD COMMENTlink written 16 months ago by elite4200
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