genomesim: A function to simulate QTL and/or SNP data.

In pedantics: Functions to Facilitate Power and Sensitivity Analyses for Genetic Studies of Natural Populations

Description

Simulates a chromosome of arbitrary length with arbitrary numbers, types, and spacings of genetic loci over arbitrary pedigrees.

Usage

genomesim(pedigree, founders=NULL, positions=NULL, initHe=NULL, 
             mutationType=NULL, mutationRate=NULL, phenotyped=NULL, 
             founderHaplotypes=NULL, genotyped=NULL, returnG='n',
             initFreqs=NULL)

Arguments

pedigree	A pedigree
founders	A vector of indicator variables denoting founder status (1=founder, 0=non-founder)
positions	Genome locations in cM for markers
initHe	Initial levels of expected heterozygosity
mutationType	A vector of locus types - see details
mutationRate	A vector of mutation rates
founderHaplotypes	A matrix or dataframe containing founder haplotypes
phenotyped	A vector of IDs of those individuals for which to return phenotypic data
genotyped	A vector of IDs of those individuals for which to return genotypic data
returnG	If 'y' then genotypic data for all loci (including cIAM loci) will be returned.
initFreqs	A list of allele frequencies for all loci. If initFreqs is specified, it will override information from initHe. extractA from package MasterBayes can be used to obtain obtain initFreqs form a sample of genotypes. For cIAM loci, allele names in initFreqs should be allelic substitution effects.

Details

Valid mutation types are ‘Micro’, ‘Dom’, ‘dIAM’ and ‘cIAM’, for microsatellite, dominant (AFLP), discrete infinite alleles mutation model loci (SNPs), and continuous infinite alleles mutation model loci (polymorphisms effecting phenotypic variation). cIAM loci have mutational allelic substitution effects taken drawn from a normal distribution with mean 0 and variance 1.

Value

Phenotypes	A vector of phenotypes. Calculated as the sum of all allelic effects. Scaling is currently left to be done post-hoc.
MarkerData	A vector of marker genotypes, i.e. alleles at all loci except those designated ‘cIAM’

Author(s)

Michael Morrissey [e-mail]

References

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.

See Also

phensim

Examples

testData<-as.data.frame(matrix(c(
1,	NA,	NA,	1,	1,	1,	2,	2,
2,	NA,	NA,	1,	1,	1,	2,	2,
3,	NA,	NA,	1,	1,	1,	2,	2,
4,	NA,	NA,	1,	0,	1,	2,	2,
5,	NA,	NA,	1,	0,	1,	2,	2,
6,	1,	4,	0,	-1,	2,	3,	3,
7,	1,	4,	0,	-1,	2,	3,	3,
8,	1,	4,	0,	-1,	2,	3,	3,
9,	1,	4,	0,	-1,	2,	3,	3,
10,	2,	5,	0,	-1,	2,	3,	3,
11,	2,	5,	0,	-1,	2,	3,	3,
12,	2,	5,	0,	-1,	2,	3,	3,
13,	2,	5,	0,	-1,	2,	3,	3,
14,	3,	5,	0,	-1,	2,	3,	3,
15,	3,	5,	0,	-1,	2,	3,	3,
16,	3,	5,	0,	-1,	2,	3,	3,
17,	3,	5,	0,	-1,	2,	3,	3),
17,8,byrow=TRUE))

names(testData)<-c("id","dam","sire","founder","sex",
                                   "cohort","first","last")
pedigree<-as.data.frame(cbind(testData$id,testData$dam,
                                            testData$sire))
for(x in 1:3) pedigree[,x]<-as.factor(pedigree[,x])
names(pedigree)<-c("id","dam","sire")
pedigree

##make up some microsatellite and gene allele frquencies:
sampleGenotypes<-as.data.frame(matrix(c(
                   1,2,-1.32,0.21,2,1,0.21,0.21),2,4,byrow=TRUE))
testFreqs<-extractA(sampleGenotypes)

## note that alleles at the gene locus are given as their
## allelic substitution effects:
testFreqs

## simulate data for these indivdiuals based on a single QTL 
## with two equally alleles with balanced frequencies in the 
## founders, linked (2 cM) to a highly  polymorphic microsatellite:
genomesim(pedigree=pedigree,founders=testData$founder,positions=c(0,2),
     mutationType=c('Micro','cIAM'),mutationRate=c(0,0),
     initFreqs=testFreqs,returnG='y')
## since we specified returnG='y', we can check that 
## the phenotypes add up to the
## allelic substitution effects for the second locus.

pedantics documentation built on May 1, 2019, 10:54 p.m.