Question: Scaling and centering of SNP genotype data in .bed format in r for use in PCA?
gravatar for bntjoanne
6 months ago by
bntjoanne10 wrote:

Hello. I would like to do some outlier detection on my SNP data. I am using pcadapt in r and import my .bed file using filename <- read.pcadapt(path_to_file, type = "bed"). In the pcadapt manual, it says "a principal component analysis is performed on the scaled and centered genotype data".

Does anyone know how to suitably scale and centre the .bed file in r in preparation for outlier analysis? Or even in plink?

Thanks in advance.

bed snp pca R pcadapt • 187 views
ADD COMMENTlink written 6 months ago by bntjoanne10
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