Input 1. PhenotypeSimulator now includes readStandardGenotypes which can read externally simulated or user-provided genotypes in plink, genome, oxgen (hapgen/impute2), bimbam or simple delimited format. 1. A user-specified correlation matrix can be provided for the simulation of the correlatedBdEffects. 1. Short option flags for command-line use of PhenotypeSimulator were removed.
Output 1. PhenotypeSimulator provides the option to save the simulated phenotypes and genotypes in formats compatible with a number of commonly used genetic association software (gemma, bimbam, plink, snptest) via writeStandardOutput. 1. Intermediate phenotype components are now saved per default. 1. Saving additional subsets of the simulated data has been removed.
Variance components 1. Genotype simulation and kinship estimation: functions for genotype simulation and kinship estimation have been rewritten for significant speed-ups of the computation time benchmarking.
geneticFixedEffects and noiseFixedEffects:
The effect size distributions of the shared effects are now modelled as the product of two exponential distributions (to yield an approximately uniform distributions) or the product of a normal distribution with user-specified parameters and a standard normal distribution.
The independent effects can now be specified to affect the same subset or different subsets of traits (via keepSameIndependent).
The overall number of traits affected by the effects can now be specified via pTraitsAffected.
correlatedBgEffects: the additional correlation between the traits can be specified by the user by providing an external correlation matrix.
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