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NEWS.md

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PhenotypeSimulator 0.3.4

Minor changes

  1. Fixed missing --genotypefile flag issue 27
  2. Update vignettes with new location for impute files and commands to get the CEU samples issue 24, thanks to @zfuller5280 for the suggestion!)
  3. Standardise genotypes on row with major alleles issue 21. Thank you for the detailed bug report by @alanw1!
  4. Add option to imput missing genotypes to standardise genotype function; otherwise, if genotypes are missing, function will fail issue 17
  5. Fix function description and passing of SNP IDs in readStandardGenotypes with delim option issue 25, thanks @BSchmidt1.

PhenotypeSimulator 0.3.3

Minor changes

  1. Fixed bug that failed to return causal SNP name when only one SNP was chosen to be causal issue 13.

PhenotypeSimulator 0.3.2

Minor changes

  1. 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 10
  2. Fixed bug for reading external genotypes file issue 9

PhenotypeSimulator 0.3.1

Minor changes

  1. Adapted output file names for genotypes consistent with other filenames from genotypes.txt to Genotypes.txt

PhenotypeSimulator 0.3.0

Major changes

  1. 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
  2. Replace parameter 'oxgen' in readStandardGenotypes and getCausalSNPs with 'format' - ensures proper specification of genotype format for all cases.

Minor changes

  1. In addition to full kinship, savePheno and writeStandardOutput write eigenvalues and eigenvalues of kinship matrix.
  2. Output file names have been made more consistent in savePheno and writeStandardOutput.
  3. Causal SNPs are now also saved in specified standard output format.
  4. LiMMBo has been added as output format in savePheno and writeStandardOutput(LiMMBo format)

PhenotypeSimulator 0.2.2

Minor changes

  1. Update readStandardGenotypes to be compatible with latest release of data.table (v1.11.2), see here

PhenotypeSimulator 0.2.1

Minor changes

  1. Additional tests for compatibility of input parameters with variance components functions, genotype functions and output functions.
  2. Bug fix in output function: savePheno now properly saves kinship matrix as .rds.

PhenotypeSimulator 0.2.0

Major changes

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.
  2. A user-specified correlation matrix can be provided for the simulation of the correlatedBdEffects.
  3. 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.
  2. Intermediate phenotype components are now saved per default.
  3. 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.

  2. geneticFixedEffects and noiseFixedEffects:

    1. 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.

    2. The independent effects can now be specified to affect the same subset or different subsets of traits (via keepSameIndependent).

    3. The overall number of traits affected by the effects can now be specified via pTraitsAffected.

  3. correlatedBgEffects: the additional correlation between the traits can be specified by the user by providing an external correlation matrix.