Genotypes are standardised as described in Yang et al: snp_standardised = (snp - 2 * ref_allele_freq)/ sqrt(2 * ref_allele_freq * alt_allele_freq).
standardiseGenotypes(geno, impute = FALSE)
| geno | [N x NrSNP] Matrix/dataframe of genotypes [integer]/[double]. |
|---|---|
| impute | [logical] Indicating if missing genotypes should be imputed; if
set FALSE and data contains missing values, |
[N x NrSNP] Matrix of standardised genotypes [double].
Missing genotypes can be mean-imputed and rounded to nearest integer
before standardisation. If genotypes contain missing values and impute is set
to FALSE, standardiseGenotypes will return an error.
Yang, J., Lee, S.H., Goddard, M.E., Visscher, P.M. (2011) GCTA: a tool for genome-wide complex trait analysis, AJHG: 88