expectedGenotypes {genetics} | R Documentation |
expectedGenotypes
constructs expected genotypes according to
known allele variants, which can be quite tedious with large number of
allele variants. It can handle different level of ploidy.
expectedGenotypes(x, alleles=allele.names(x), ploidy=2, sort=TRUE, haplotype=FALSE) expectedHaplotypes(x, alleles=allele.names(x), ploidy=2, sort=TRUE, haplotype=TRUE)
x |
genotype or haplotype |
alleles |
character, vector of allele names |
ploidy |
numeric, number of chromosome sets i.e. 2 for human autosomal genes |
sort |
logical, sort genotypes according to order of alleles in
alleles argument |
haplotype |
logical, construct haplotypes i.e. ordered genotype |
At least one of x
or alleles
must be given.
expectedHaplotypes()
just calls expectedGenotypes()
with
argument haplotype=TRUE
.
A character vector with genotype names as "alele1/alele2" for diploid example. Length of output is (n*(n+1))/2 for genotype (unordered genotype) and n*n for haplotype (ordered genotype) for n allele variants.
Gregor Gorjanc
## On genotype prp <- c("ARQ/ARQ", "ARQ/ARQ", "ARR/ARQ", "AHQ/ARQ", "ARQ/ARQ") alleles <- c("ARR", "AHQ", "ARH", "ARQ", "VRR", "VRQ") expectedGenotypes(as.genotype(prp)) expectedGenotypes(as.genotype(prp, alleles=alleles)) expectedGenotypes(as.genotype(prp, alleles=alleles, reorder="yes")) ## Only allele names expectedGenotypes(alleles=alleles) expectedGenotypes(alleles=alleles, ploidy=4) ## Haplotype expectedHaplotypes(alleles=alleles) expectedHaplotypes(alleles=alleles, ploidy=4)[1:20]