simulN {simulMGF} | R Documentation |
Function to simulate a SNP matrix, a phenotypic trait and the effects of associated SNPs.
Description
This function simulate a SNP matrix (coded as 0, 1, 2) and traits with a selected number of QTLs and their effects that will be sampled from a Normal distribution.
Usage
simulN(Nind, Nmarkers, Nqtl, Esigma, Pmean, Perror)
Arguments
Nind |
number of individuals to simulate. |
Nmarkers |
number of SNP markers to generate. |
Nqtl |
number of QTLs controlling the trait. |
Esigma |
standard deviation of effects with distribution N~(0,Esigma^2). |
Pmean |
phenotype mean. |
Perror |
standard deviation of error (portion of phenotype not explained by genomic information). |
Details
Genotypic data is simulated as the round value sampled from an uniform distribution with interval (-.5,2.5). Phenotypic data are obtained as a linear function defined by:
y = Pmean + \sum QTN*Meffects + Perror
Value
An object of class list containing the SNP matrix, the trait, the markers associated and their effects.
geno |
SNP matrix generated. |
pheno |
vector with the trait values simulated. |
QTN |
column in the SNP matrix with the SNP associated. |
Meffects |
effects of the associated SNPs. |
Note
The genotype is simulated in the same way of simGeno function. The trait, QTLs and their effects are simulated in the same way of simPheno function.
Author(s)
Martin Nahuel Garcia <orcid:0000-0001-5760-986X>
References
Wu, R., Ma, C., & Casella, G. (2007). Statistical genetics of quantitative traits: linkage, maps and QTL. Springer Science & Business Media.
See Also
simGeno, simPheno, simulU
Examples
set.seed(123)
simulN(100, 1000, 50, .9, 12, .5)
#[1] "nsimout was generated"
str(nsimout)
#List of 4
#$ geno : num [1:100, 1:1000] 0 2 1 2 2 0 1 2 1 1 ...
#$ pheno : num [1:100, 1] 25.4 21.6 16 13.8 19.4 ...
#$ QTN : int [1:50] 568 474 529 349 45 732 416 51 413 514 ...
#$ Meffects: num [1:50] 0.2696 -0.1552 1.0192 0.0209 1.2023 ...