standardiseGenotypes: Standardise genotypes.
In PhenotypeSimulator: Flexible Phenotype Simulation from Different Genetic and Noise Models
Description
Usage
Arguments
Details
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
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
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 July 16, 2021, 5:06 p.m.
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Description Usage Arguments Details 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 | 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, |
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
Examples
1 2 | geno <- cbind(rbinom(2000, 2, 0.3), rbinom(2000, 2, 0.4),rbinom(2000, 2, 0.5))
geno_sd <- standardiseGenotypes(geno)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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