rbm.haplos.freqs: Simulation of genetic data based on haplotypic frequencies

In Ravages: Rare Variant Analysis and Genetic Simulations

Simulation of genetic data based on haplotypic frequencies

Description

Simulates genetic data with respect to allele frequency spectrum and linkage disequilibrium pattern observed on given haplotypes and their frequencies

Usage

  rbm.haplos.freqs(haplos, freqs, size, replicates)

Arguments

haplos	A matrix of haplotypes with one row per haplotype and one column per variant
freqs	A matrix of haplotypes frequencies in each group of individuals
size	The sizes of each group of individuals
replicates	The number of simulations to perform

Details

Simulations are performed to respect linkage disequilibrium pattern and allelic frequency spectrum in each group of individuals The phenotypic values will be the colnames of freqs and stored in @ped$pheno. The simulation number will be in @snps$genomic.region.

Value

x	A bed matrix with simulated genotypes

Examples

  #Simulations of 5 groups of individuals with haplotypes frequencies
  #from the 5 EUR populations

  #Load LCT dataset for haplotype matrix
  data(LCT.haplotypes)
  #Haplotypes for the variants in the LCT gene in the EUR population
  LCT.gene.hap <- LCT.hap[which(LCT.sample$super.population=="EUR"),
                         which(LCT.snps$pos>=136545410 & LCT.snps$pos<=136594750)]

  #Individuals from EUR
  LCT.sample.EUR <- subset(LCT.sample, super.population=="EUR")
  #Matrix of haplotypic frequencies
  LCT.freqs <- sapply(unique(LCT.sample.EUR$population), function(z) 
                      ifelse(LCT.sample.EUR$population==z, 
                             1/table(LCT.sample.EUR$population)[z], 0))

  #Simulation of genetic data for five groups of 50 individuals
  x <- rbm.haplos.freqs(haplos=LCT.gene.hap, freqs=LCT.freqs, size=rep(50,5), replicates=5)

Ravages documentation built on April 1, 2023, 12:08 a.m.