standardiseGenotypes {PhenotypeSimulator}

Standardise genotypes.

Description

Genotypes are standardised as described in Yang et al: snp_standardised = (snp - 2 * ref_allele_freq)/ sqrt(2 * ref_allele_freq * alt_allele_freq).

Usage

standardiseGenotypes(geno, impute = FALSE)

Arguments

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, standardiseGenotypes will return an error.

Details

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.

Value

[N x NrSNP] Matrix of standardised genotypes [double].

References

Yang, J., Lee, S.H., Goddard, M.E., Visscher, P.M. (2011) GCTA: a tool for genome-wide complex trait analysis, AJHG: 88

See Also

getAlleleFrequencies

Examples

geno <- cbind(rbinom(2000, 2, 0.3), rbinom(2000, 2, 0.4),rbinom(2000, 2, 0.5))
geno_sd <- standardiseGenotypes(geno)