simulGenosDoseStruct: Genotypes

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Genotypes

Description

Simulate SNP genotypes as allele dose additively encoded, i.e. 0,1,2, using correlated allele frequencies to mimick genetic structure.

Usage

simulGenosDoseStruct(
  nb.genos = c(100, 120, 80),
  nb.snps = 1000,
  div.pops = diag(3) * 0.5 + 0.5,
  geno.ids = NULL,
  snp.ids = NULL
)

Arguments

nb.genos	number of genotypes (i.e. individuals) per population
nb.snps	number of SNPs
div.pops	matrix of divergence among populations, with a diagonal of 1's; the closer off-diagonal values are from 1; the weaker the divergence; the further, the stronger
geno.ids	vector of genotype identifiers (if NULL, will be "geno001", etc)
snp.ids	vector of SNP identifiers (if NULL, will be "snp001", etc)

Value

matrix with genotypes in rows and SNPs in columns

Author(s)

Andres Legarra [aut], Timothee Flutre [ctb]

Examples

## Not run: 
## weak divergences among populations:
weak.div.pops <- diag(3)
weak.div.pops[upper.tri(weak.div.pops)] <- 0.9
weak.div.pops[lower.tri(weak.div.pops)] <- weak.div.pops[upper.tri(weak.div.pops)]
weak.div.pops

## strong divergences among populations:
strong.div.pops <- diag(3)
strong.div.pops[upper.tri(strong.div.pops)] <- 0.5
strong.div.pops[lower.tri(strong.div.pops)] <- strong.div.pops[upper.tri(strong.div.pops)]
strong.div.pops

X <- simulGenosDoseStruct(div.pops=weak.div.pops)
A <- estimGenRel(X)
imageWithScale(A, "Weak divergence")

X <- simulGenosDoseStruct(div.pops=strong.div.pops)
A <- estimGenRel(X)
imageWithScale(A, "Strong divergence")

## End(Not run)

timflutre/rutilstimflutre documentation built on Feb. 12, 2025, 11:35 p.m.