| hwp {GeneticsPed} | R Documentation |
gpLong2Wide changes data.frame with genotype probabilities in
long form (one genotype per row) to wide form (one individual per row)
for use in gpi.
hwp calculates genotype probabilities according to Hardy-Weinberg
law for use in gpi.
gpLong2Wide(x, id, genotype, prob, trim=TRUE) hwp(x, trim=TRUE)
x |
data.frame for |
id |
character, column name in |
genotype |
character, column name in |
prob |
character, column name in |
trim |
logical, remove last column (for |
Hardy-Weinberg probabilities for a gene with two alleles A and B, with probabilities Pr(A) and Pr(B) are:
Pr(AA) = Pr(A)^2
Pr(AB) = 2 * Pr(A) * Pr(A)
Pr(BB) = Pr(B)^2
gpLong2Wide returns a matrix with number of rows equal to number
of individuals and number of columns equal to number of possible
genotypes.
hwp returns a vector with Hardy-Weinberg genotype probabilities.
Gregor Gorjanc
gpi,
genotype,
expectedGenotypes
if(require(genetics)) {
gen <- genotype(c("A/A", "A/B"))
hwp(x=gen)
hwp(x=gen, trim=FALSE)
}