simcross (version 0.6)

convert2geno_allchr: Convert continuous allele information into marker genotypes for multiple chromosomes

Description

Wrap up of convert2geno to adequate multiple chromosomes.

Usage

convert2geno_allchr(
  xodat,
  map,
  id = NULL,
  founder_geno = NULL,
  return.matrix = TRUE,
  shift_map = FALSE
)

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 there are more than two founders and founder_geno are letters, the result is a character matrix, too.

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.

Arguments

xodat

The sort of detailed genotype/crossover data generated by sim_from_pedigree_allchr()

map

marker locations, a list with elements for each chromosome

id

ids for which individuals genotypes is desired

founder_geno

Optional list of matrices (one per chromosome) of size n_founders x n_markers, with the 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 (in the case of 8 founders), results are two-letter genotypes AA-HH with 36 possible values.

return.matrix

If FALSE, the result is a list of length n_chrs, otherwise it is converted into a matrix if size length(id) x n_markers.

shift_map

If TRUE, shift genetic map to start at 0

See Also

convert2geno()

Examples

library(qtl)
# marker map
map <- sim.map(len=rep(100, 19), n.mar=10, include.x=FALSE)
# simulate AIL pedigree
tab <- sim_ail_pedigree(12, 30)
# simulate data from that pedigree
dat <- sim_from_pedigree_allchr(tab, map)
names(map) <- paste0("marker", seq(along=map))
# convert data to marker genotypes
id <- which(tab[, "gen"]==12)
geno <- convert2geno_allchr(dat, map, id)