R/HWE.R

In thibautjombart/adegenet: Exploratory Analysis of Genetic and Genomic Data

##################
# HWE.test.genind
##################

HWE.test.genind <- function(x,pop=NULL,permut=FALSE,nsim=1999,hide.NA=TRUE,res.type=c("full","matrix")){

    message("As of adegenet_1.5-0, this function has been removed and is replaced by 'hw.test' in the package 'pegas'")

  ## if(!is.genind(x)) stop("x is not a valid genind object")
  ## if(x@ploidy != as.integer(2)) stop("not implemented for non-diploid genotypes")
  ## checkType(x)

  ## if(is.null(pop)) pop <- x@pop
  ## if(is.null(pop)) pop <- as.factor(rep("P1",nrow(x@tab)))
  ## res.type <- tolower(res.type[1])
  ## if(res.type != "full" && res.type != "matrix") stop("unknown res.type specified.")

  ## kGen <- genind2genotype(x,pop=pop,res.type="list")

  ## # ftest tests HWE for a locus and a population
  ## ftest <- function(vec,permut=permut,nperm=nsim){
  ##   temp <- unique(vec)
  ##   temp <- temp[!is.na(temp)]
  ##   if(length(temp) < 2) return(NA)
  ##   if(res.type=="full") {
  ##     res <- HWE.chisq(vec, simulate.p.value=permut, B=nperm)
  ##   } else {
  ##     res <- HWE.chisq(genotype(vec), simulate.p.value=permut, B=nperm)$p.value
  ##   }
  ##   return(res)
  ## }

  ## res <- lapply(kGen,function(e) lapply(e,ftest,permut,nsim))

  ## # clean non-tested elements in the results list
  ## if(hide.NA && res.type=="full"){
  ##   newres=list()
  ##   tokeep <- which(unlist(lapply(res,function(e) !all(is.na(e)))))
  ##   if(length(tokeep) > 0) for(i in 1:length(tokeep)) {newres[[i]] <- res[[tokeep[i]]]}
  ##   newres <- lapply(newres,function(e) {e[!is.na(e)] })
  ##   names(newres) <- names(res)[tokeep]
  ##   res <- newres
  ## }

  ## if(res.type=="matrix"){
  ##   res <- as.data.frame(lapply(res,unlist))
  ##   rnam <- rownames(res)
  ##   rownames(res) <- gsub(".X-squared","",rnam)
  ##   res <- as.matrix(res)
  ## }

  ## return(res)
}