standardiseGenotypes: Standardise genotypes

Description Usage Arguments Value References See Also Examples

View source: R/genotypeFunctions.R

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

1

Arguments

geno

[N x NrSNP] Matrix/dataframe of genotypes [integer]/[double].

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

1
2
geno <- cbind(rbinom(2000, 2, 0.3), rbinom(2000, 2, 0.4),rbinom(2000, 2, 0.5))
geno_sd <- standardiseGenotypes(geno)

PhenotypeSimulator documentation built on May 14, 2018, 1:04 a.m.