NEWS.md
Add option for non-linear transformation of simulated phenotypes: function (transformNonlinear)[https://github.com/HannahVMeyer/PhenotypeSimulator/blob/master/R/createphenotypeFunctions.R], accessible from runSimulation. Both transformed and original phenotypes are automatically returned with savePheno
Replace parameter ‘oxgen’ in readStandardGenotypes and getCausalSNPs with ‘format’ - ensures proper specification of genotype format for all cases.
In addition to full kinship, savePheno and writeStandardOutput write eigenvalues and eigenvalues of kinship matrix.
Output file names have been made more consistent in savePheno and writeStandardOutput.
Causal SNPs are now also saved in specified standard output format.
LiMMBo has been added as output format in savePheno and writeStandardOutput(LiMMBo format)
Input
Output
Variance components
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.