Sim.SG.Data: Simulate genotypes over a single year

In patbarry6/PseudoBabies: Assess power of genetic markers for parentage through simulation

Description

This function allows you to simulate multilocus genotypes under the assumption of completely random mating for a single year

Usage

Sim.SG.Data(
  Founders = "FoundersCompleteGenotypes.csv",
  Markerfile = "MarkerPanels.csv",
  NumSNPs = 93,
  NumuSats = 12,
  NB = 650,
  StartYear = as.numeric(format(Sys.Date(), "%Y")),
  nSim = 10,
  Geno_Error = F,
  ErrorVals,
  Miss_data = F,
  MissingVec,
  Programs = c("FRANz", "Colony"),
  SexInf,
  perl.dir,
  GPHomogeneity = FALSE,
  OffspringDist = "Poisson",
  SexInfo = F,
  lambda,
  Umin = 0,
  Umax = 1,
  nBprob,
  nBsize,
  ztnbprob,
  ztnbsize,
  MatingStr = "Polygyny"
)

Arguments

Founders	.csv file containing the genotypes to use for initiating the simulation. Use function CompleteGenotypes to remove missing data before performing simulations.
Markerfile	.csv for marker panels that will be evaluated.
NumSNPs	number of SNP markers.
NumuSats	number of microsatellite markers.
NB	number of crosses to perform. Defaults to 100.
StartYear	What year should the simulation start? Defaults to current year.
nSim	How many replicate simulations would you like to do? Defaults to 10.
Geno_Error	Would you like to add genotyping error to the simualated data? Defaults to FALSE
ErrorVals	How many different values of genotyping error for simulations. Required if Geno_Error=TRUE. Values specified in Loci_error.csv
Miss_data	Would you like to add missing data to the simulations? Defaults to FALSE
MissingVec	A vector of values for the percent of missing data in the input file. Required if Miss_data=TRUE.
Programs	Which programs would you like to create input files for? Defaults to c('FRANz','Colony')
SexInf	Use the sex of individuals in the parentage inference program
perl.dir	Full path to .csv.pl perl script distributed with FRANz for formatting input files. Required when FRANz is specified as a Program argument
GPHomogeneity	A logical to indicate if genepop should be run to compare the allele frequency distribution for all simulated datasets with the founders dataset. Defaults to FALSE
OffspringDist	What distribution should we use for the number of offspring produced for each cross. Options are Uniform (specify a min and a max), NegativeBinomial (specify a prob for the scale parameter see NegBinomial options), and Poisson (specify lambda).
SexInfo	Does your dataset have information on sex?
MatingStr	Should the simulation allow for polygamy, polygyny, polandry, or monogamy?

Examples

Sim_SG_Data()

patbarry6/PseudoBabies documentation built on Dec. 22, 2021, 6:41 a.m.