convert2geno: Convert continuous allele information into marker genotypes

In kbroman/simcross: Simulate Experimental Crosses

Convert continuous allele information into marker genotypes

Description

Convert the continuous crossover location information produced by sim_from_pedigree to marker genotypes

Usage

convert2geno(xodat, map, founder_geno = NULL, shift_map = FALSE)

Arguments

xodat	The sort of detailed genotype/crossover data generated by sim_from_pedigree()
map	vector of marker locations; can also be a list of such vectors (one per chromosome), in which case xodat and founder_geno must be lists with the same length.
founder_geno	Optional matrix (size n_founders x length(map)) of founder genotypes. If coded as 1/2 (or 1/3), results are 1/2/3 genotypes. If coded as A/T/G/C/N, results are A/T/G/C/N/H genotypes. If coded as letters A-H for the 8 founders, results are two-letter genotypes AA-HH with 36 possible values.
shift_map	If TRUE, shift genetic map to start at 0

Value

If founder_geno is provided or there are just two founders, the result is a numeric matrix of genotypes, individuals x markers, with genotypes 1/2/3 codes for 11/12/22 genotypes.

If founder_geno is not provided and there are more than two founders, the result is a 3-dimensional array, individuals x markers x alleles, with the third dimensional corresponding to the maternal and paternal allele.

If the input map is a list (the components being chromosomes), then xodat and founder_geno must be lists of the same length, and the result will be a list of matrices.

See Also

get_geno(), sim_from_pedigree()

Examples

# simulate AIL pedigree
tab <- sim_ail_pedigree(12, 30)
# simulate data from that pedigree
dat <- sim_from_pedigree(tab)
# marker map (could also use sim.map in R/qtl)
map <- seq(0, 100, by=5)
names(map) <- paste0("marker", seq(along=map))
# convert data to marker genotypes
geno <- convert2geno(dat, map)


# AIL with multiple chromosomes
dat <- sim_from_pedigree(tab, c("1"=100, "2"=75, "X"=100), xchr="X")
# marker map
multmap <- list("1"=seq(0, 100, by=5),
                "2"=seq(0, 75, by=5),
                "X"=seq(0, 100, by=5))
for(i in 1:3)
  names(multmap[[i]]) <- paste0("marker", i, "_", 1:length(map[[i]]))
geno <- convert2geno(dat, multmap)

# simulate DO pedigree
tab <- sim_do_pedigree(8)
# simulate data from that pedigree
dat <- sim_from_pedigree(tab)
# simulate founder snp alleles
fg <- matrix(sample(1:2, 8*length(map), repl=TRUE), nrow=8)
# for DO, need female & male founders (to deal with X chr)
fg <- rbind(fg, fg)
# convert dat to SNP genotypes
geno <- convert2geno(dat, map, fg)
# if fg not provided, result is a 3d array
genoarray <- convert2geno(dat, map)

kbroman/simcross documentation built on Jan. 13, 2024, 10:31 p.m.