populate.snp: Populate SNPs.
In bowenwang7/r3: Realized Relatedness Estimation and Simulation

Description Usage Arguments Details Value Examples

populate.snp assigns alleles to markers, given inheritance information and founder haplotypes.

1 2	populate.snp(inheritance, haplotype, marker, member.index = NULL, output.allele = TRUE, output.haplotype = FALSE)

`inheritance`	list of numeric matrices.
`haplotype`	numeric matrix.
`marker`	numeric vector.
`member.index`	integer vector.
`output.allele`	logical.
`output.haplotype`	logical.

inheritance is a list of matrices produced by, e.g., sim.recomb. Each matrix contains a column of founder genome labels and a column of recombination breakpoints for the corresponding meiosis.

haplotype is a numeric matrix. The matrix is number of haplotypes by number of markers in dimension. Standard coding in this package is 1 for reference allele and 2 for alternate allele. This coding is required when output.allele = FALSE. Input data with different coding of alleles can be recoded using recode.snpdata. Number of haplotypes cannot be fewer than the number of founder genome labels in inheritance. The haplotypes will be assigned to each founder genome label in given order.

marker is a vector of marker genetic positions in Haldane centiMorgan in ascending order. Range of marker positions cannot exceed range covered by inheritance.

member.index contains indices of members in the pedigree that we wish to output data. Default value is FALSE, in which case marker data on everyone will be produced. get.pedindex can help find indices given member ID.

output.allele determines if one or two numbers will be used to represent data at each marker. Default is TRUE, in which case marker data is represented by two ordered (paternal first) alleles. Otherwise marker data is represented by a single number (0, 1 or 2) of reference alleles.

output.haplotype determines if haplotype data are separate in output. It is only used when output.allele = TRUE. Default value is FALSE, in which case each row in the output matrix represents ordered genotypes from all markers of the same individual. Otherwise each row in the output matrix represents a parental haplotype.

A matrix of genotypic/haplotypic data. The matrix is in individual major, where marker data for each individual/meiosis are found on the same row. Exact format of the matrix depends on various input arguments.

# a simple pedigree with sibling marriage
pedigree = as.character(rep(1, 5))
member = as.character(c(11, 12, 21, 22, 31))
sex = as.numeric(c(1, 2, 1, 2, 1))
father = as.character(c(NA, NA, 11, 11, 21))
mother = as.character(c(NA, NA, 12, 12, 22))
pedinfo = data.frame(pedigree, member, sex, father, mother, stringsAsFactors = FALSE)

L = 100.0 # segment length
nsnp = 10 # number of SNPs
nhaplo = 4 # number of founder haplotypes
inher = sim.recomb(pedinfo, L)
haplo = matrix(c(3,4,4,4), nhaplo, nsnp)
marker = sort(runif(nsnp, 0, L))

# output genotype data for the 4th and 5th member
# of pedigree, genotype data displayed as two alleles
populate.snp(inher, haplo, marker, c(4, 5))

# output haplotype data for the 4th and 5th member of pedigree
populate.snp(inher, haplo, marker,c(4, 5), output.haplotype = TRUE)

# output genotype data for all members, genotype data
# displayed as counts of reference alleles
geno = recode.snpdata(haplo, input.haplotype = TRUE, output.haplotype = TRUE)[[1]]
populate.snp(inher, geno, marker, output.allele = FALSE)