alleSimulator {alleHap} | R Documentation |
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.
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)
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. |
Families' genotypes and haplotypes.
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).
## 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