Simulation of Pleiotropic, Linked and Epistatic Phenotypes
Calculate genetic value based on QTN objects.
Calculate genetic value based on QTN objects.
Select SNPs to be assigned as QTNs: To be included LD, FST
Simulation of single/multiple traits under different models and geneti...
Function used by create_phenotypes to load marker dataset.
Calculate genetic value based on QTN objects.
Generate a numeric (dosage) HapMap file
obtain a positive definite matrix
Converts character SNP genotype to numerical (-1, 0, 1) were 1 is the ...
Generate environmental effects based on a given heritability
Select SNPs to be assigned as QTNs
Select SNPs to be assigned as QTNs
Select SNPs to be assigned as QTNs
Select SNPs to be assigned as QTNs.
The number of studies involving correlated traits and the availability of tools to handle this type of data has increased considerably in the last decade. With such a demand, we need tools for testing hypotheses related to single and multi-trait (correlated) phenotypes based on many genetic settings. Thus, we implemented various options for simulation of pleiotropy and Linkage Disequilibrium under additive, dominance and epistatic models. The simulation currently takes a marker data set as an input and then uses it for simulating multiple traits as described in Fernandes and Lipka (2020) <doi:10.1186/s12859-020-03804-y>.
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