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.