- Fixed missing –genotypefile flag issue
- Update vignettes with new location for impute files and commands to
get the CEU samples issue
24, thanks to @zfuller5280 for the suggestion!)
- Standardise genotypes on row with major alleles issue
21. Thank you for the detailed bug report by @alanw1!
- Add option to imput missing genotypes to standardise genotype
function; otherwise, if genotypes are missing, function will fail issue
- Fix function description and passing of SNP IDs in
readStandardGenotypes with delim option issue
25, thanks @BSchmidt1.
- Fixed bug that failed to return causal SNP name when only one SNP
was chosen to be causal issue
- Option for external, delimited genotype file to contain a header;
additional checks to make sure the right data is received when sampling
from the genotypes file issue
- Fixed bug for reading external genotypes file issue
- Adapted output file names for genotypes consistent with other
filenames from genotypes.txt to Genotypes.txt
- Add option for non-linear transformation of simulated phenotypes:
accessible from runSimulation.
Both transformed and original phenotypes are automatically returned with
- Replace parameter ‘oxgen’ in readStandardGenotypes
with ‘format’ - ensures proper specification of genotype format for all
cases. ## Minor changes
- In addition to full kinship, savePheno
write eigenvalues and eigenvalues of kinship matrix.
- Output file names have been made more consistent in savePheno
- Causal SNPs are now also saved in specified standard output
- LiMMBo has been added as output format in savePheno
and writeStandardOutput(LiMMBo format)
- Update readStandardGenotypes to be compatible with latest release of
data.table (v1.11.2), see here
- Additional tests for compatibility of input parameters with variance
components functions, genotype functions and output functions.
- Bug fix in output function: savePheno now properly saves kinship
matrix as .rds.
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
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
The independent effects can now be specified to affect the same
subset or different subsets of traits (via
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