Nothing
snphwe <- function(g) {
gt <- table(g) ## assume sorting works, e.g. AA/AC/CC or 0/1/2 but not AA/AC/CA/CC
if (length(gt) <= 2) return(p = 1.)
if (length(gt) == 3) return(p = snphweCounts(gt[2], gt[1], gt[3]))
##warning("cannot calculate exact p-value for >3 genotypes")
return(NA)
}
## This code implements an exact SNP test of Hardy-Weinberg Equilibrium as described in
## Wigginton, JE, Cutler, DJ, and Abecasis, GR (2005) A Note on Exact Tests of
## Hardy-Weinberg Equilibrium. American Journal of Human Genetics. 76:(5) 887-893
## Original code of Wiggington, Cutler and Abecasis
## modified so that:
## 0. function name is snphweCounts instead of SNPHWE
## 1. error conditions cause stop with informative message
## instead of returning -1
## 2. explicit return statement for computed p-value
snphweCounts <- function(obs_hets, obs_hom1, obs_hom2) {
if (obs_hom1 < 0 || obs_hom2 < 0 || obs_hets < 0)
stop("genotype counts must be non-negative")
## total number of genotypes
N <- obs_hom1 + obs_hom2 + obs_hets
## rare homozygotes, common homozygotes
obs_homr <- min(obs_hom1, obs_hom2)
obs_homc <- max(obs_hom1, obs_hom2)
## number of rare allele copies
rare <- obs_homr * 2 + obs_hets
## Initialize probability array
probs <- rep(0, 1 + rare)
## Find midpoint of the distribution
mid <- floor(rare * ( 2 * N - rare) / (2 * N))
if ( (mid %% 2) != (rare %% 2) ) mid <- mid + 1
probs[mid + 1] <- 1.0
mysum <- 1.0
## Calculate probablities from midpoint down
curr_hets <- mid
curr_homr <- (rare - mid) / 2
curr_homc <- N - curr_hets - curr_homr
while ( curr_hets >= 2) {
probs[curr_hets - 1] <- probs[curr_hets + 1] * curr_hets * (curr_hets - 1.0) / (4.0 * (curr_homr + 1.0) * (curr_homc + 1.0))
mysum <- mysum + probs[curr_hets - 1]
## 2 fewer heterozygotes -> add 1 rare homozygote, 1 common homozygote
curr_hets <- curr_hets - 2
curr_homr <- curr_homr + 1
curr_homc <- curr_homc + 1
}
## Calculate probabilities from midpoint up
curr_hets <- mid
curr_homr <- (rare - mid) / 2
curr_homc <- N - curr_hets - curr_homr
while ( curr_hets <= rare - 2) {
probs[curr_hets + 3] <- probs[curr_hets + 1] * 4.0 * curr_homr * curr_homc / ((curr_hets + 2.0) * (curr_hets + 1.0))
mysum <- mysum + probs[curr_hets + 3]
## add 2 heterozygotes -> subtract 1 rare homozygtote, 1 common homozygote
curr_hets <- curr_hets + 2
curr_homr <- curr_homr - 1
curr_homc <- curr_homc - 1
}
## P-value calculation
target <- probs[obs_hets + 1]
##plo <- min(1.0, sum(probs[1:obs_hets + 1]) / mysum)
##phi <- min(1.0, sum(probs[obs_hets + 1: rare + 1]) / mysum)
## This assignment is the last statement in the fuction to ensure
## that it is used as the return value
return(p = min(1.0, sum(probs[probs <= target])/ mysum))
}
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