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agdamsbo 2018-10-08 16:36:46 +02:00
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R/hwe_sum.R
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@ -9,26 +9,18 @@
#' @examples
#' hwe_sum()
hwe_sum<-function(a1,a2,f){
## HWE summarising function, for several groups defined by factor f. Alleles are provided as vectors, a1 and a2.
hwe_sum<-function (a1, a2, f) {
require(daDoctoR)
lst <- list()
df <- data.frame(a1, a2)
source("https://raw.githubusercontent.com/agdamsbo/research/master/hwe_allele.R")
lst<-list()
df<-data.frame(cbind(a1,a2))
for (i in 1:length(ls<-split(df,f))){
grp<-names(ls)[i]
obs<-data.frame(hwe_allele(ls[[i]][,1],ls[[i]][,2])[[c("observed.dist")]])
pval<-round(hwe_allele(ls[[i]][,1],ls[[i]][,2])[[c("p.value")]],3)
prnt<-paste0(obs[1,]," (",obs[2,],")")
names(prnt)<-names(obs)
lst<-list(lst,grp,obs.dist=obs,print=prnt,hwe.pv=pval)
for (i in 1:length(ls <- split(df, f))) {
grp <- names(ls)[i]
obs <- data.frame(hwe_allele(ls[[i]][, 1], ls[[i]][,2])[[c("observed.dist")]])
pval <- round(hwe_allele(ls[[i]][, 1], ls[[i]][, 2])[[c("p.value")]],3)
prnt <- paste0(obs[1, ], " (", obs[2, ], ")")
names(prnt) <- names(obs)
lst <- list(lst, grp, obs.dist = obs, print = prnt,hwe.pv = pval)
}
return(lst)
return(lst)
}