microsim

0th

Percentile

Simulates microsatellite data across a pedigree.

Uses a pedgiree with parents identified for all non-founding individuas and simulates microsatellite genotypes

Keywords
datagen
Usage
microsim(pedigree, genFreqs = NULL, genotypesSample = NULL, 
        knownGenotypes = NULL,records = NULL, eRate1 = 0, 
        eRate2 = 0, eRate3 = 0)
Arguments
pedigree

A pedigree

genFreqs

(optional) A list of allele frequencies, can be produced with extractA in MasterBayes

genotypesSample

(required if genFreqs is not supplied) a sample of genotypes from which to estimate population allele frequencies

knownGenotypes

(not yet implemented) a data frame of genotypes for (potentially a subset) of founder individuals

records

Record availability, see details.

eRate1

The rate of genotypic substitution errors, i.e., when a true genotype at a given locus is replaced by a pair of alleles selected at random based on the population allele frequencies

eRate2

The rate of allelic substitution errors, i.e. when an allele is erroneously replaced at a given locus by an allele chosen at random based on the population allele frequencies

eRate3

The rate of large allele dropouts, simulated by setting the value of the larger allele at a locus to the value of the smaller allele

Details

Error rates and data availability rates can be specified as either (1) single values to be applied to all individuals and all loci, (2) as a vector the same length as the number of loci, representing locus-specific rates to be applied uniformly to all individuals, or (3) as data frames with rows for each individual and columns for each locus. In the third option, observed patterns of data availability can be simulated by supplying 0s and 1s for missing and available individual genotypes, respectively.

Value

trueGenotypes

A data frame of true genotypes

observedGenotypes

A data frame of plausible observed genotypes, given specified patterns of missingness and errors.

References

Morrissey et al. 2007. Journal of Evolutionary Biology 20:2309-2321., Morrissey, M.B, and A.J. Wilson, 2009. pedantics, an R package for pedigree-based genetic simulation, and pedigree manipulation, characterisation, and viewing. Molecular Ecology Resources.

Aliases
  • microsim
Examples
# NOT RUN {
pedigree<-as.data.frame(matrix(c(
"m1",	NA,	NA,
"m2",	NA,	NA,
"m3",	NA,	NA,
"d4",	NA,	NA,
"d5",	NA,	NA,
"o6",	"m1",	"d4",
"o7",	"m1",	"d4",
"o8",	"m1",	"d4",
"o9",	"m1",	"d4",
"o10",	"m2",	"d5",
"o11",	"m2",	"d5",
"o12",	"m2",	"d5",
"o13",	"m2",	"d5",
"o14",	"m3",	"d5",
"o15",	"m3",	"d5",
"o16",	"m3",	"d5",
"o17",	"m3",	"d5"),17,3,byrow=TRUE))
names(pedigree)<-c("id","dam","sire")
for(x in 1:3) pedigree[,x]<-as.factor(pedigree[,x])

## some sample genotypes, very simple, two markers with He = 0.5
sampleGenotypes<-as.data.frame(matrix(c(
                   1,2,1,2,2,1,2,1),2,4,byrow=TRUE))
## locus names
names(sampleGenotypes)<-c("loc1a","loc1b","loc2a","loc2b")

## simulate some genotypes
microsim(pedigree=pedigree,genotypesSample=sampleGenotypes)

# }
Documentation reproduced from package pedantics, version 1.7, License: GPL-2 | GPL-3

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