alleSimulator {alleHap}

Simulation of genetic data (alleles) and non-genetic data (family identifiers)

Description

Data simulation can be performed taking into account many different factors such as number of families to generate, number of markers (allele pairs), number of different alleles per marker, type of alleles (numeric or character), number of different haplotypes in the population, probability of parent/offspring missing genotypes, proportion of missing genotypes per individual, probability of being affected by disease and recombination rate.

Usage

alleSimulator(nFams = 2, nChildren = NULL, nMarkers = 3,
  numAllperMrk = NULL, chrAlleles = TRUE, nHaplos = 1200,
  missParProb = 0, missOffProb = 0, ungenotPars = 0, ungenotOffs = 0,
  phenProb = 0.2, recombRate = 0, invisibleOutput = TRUE)

Arguments

nFams

Number of families to generate (integer: 1..1000+)

nChildren

Number of children of each family (integer: 1..7 or NULL)

nMarkers

Number of markers or allele pairs to generate (integer: 1..1000+)

numAllperMrk

Number of different alleles per marker (vector or NULL)

chrAlleles

Should alleles be expressed as characters A,C,G,T ? (boolean: FALSE, TRUE)

nHaplos

Number of different haplotypes in the population (numeric)

missParProb

Probability of parents' missing genotype (numeric: 0..1)

missOffProb

Probability of offspring' missing genotype (numeric: 0..1)

ungenotPars

Proportion of ungenotyped parents (numeric: 0..1)

ungenotOffs

Proportion of ungenotyped offspring (numeric: 0..1)

phenProb

Phenotype probability, e.g. being affected by disease (numeric: 0..1)

recombRate

Recombination rate (numeric: 0..1)

invisibleOutput

Data are not shown by default.

Value

Families' genotypes and haplotypes.

References

Medina-Rodriguez, N. Santana A. et al. (2014) alleHap: an efficient algorithm to reconstruct zero-recombinant haplotypes from parent-offspring pedigrees. BMC Bioinformatics, 15, A6 (S-3).

Examples

## Generation of 5 simulated families with 2 children per family and 10 markers
simulatedFams <- alleSimulator(5,2,10)   # List with simulated alleles and haplotypes
simulatedFams[[1]]                       # Alleles (genotypes) of the simulated families
simulatedFams[[2]]                       # Haplotypes of the simulated families