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128 lines
3.8 KiB
R
128 lines
3.8 KiB
R
#' HWE calculation by alleles
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#'
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#' For easy calculation.
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#' @param x Allele 1.
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#' @param y Allele 2.
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#' @keywords hardy-weinberg-equllibrium
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#' @export
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hwe_allele<-function(x,y)
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{
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## Witten by Andreas Gammelgaard Damsbo, agdamsbo@pm.me, based on a non-working
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## applet at http://www.husdyr.kvl.dk/htm/kc/popgen/genetik/applets/kitest.htm
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all<-pmax(length(levels(factor(x))),length(levels(factor(y))))
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if(all==2){
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df=1
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## Biallellic system, df=1
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al1<-factor(x,labels=c("p","q"))
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al2<-factor(y,labels=c("p","q"))
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snp<-paste(al1,al2,sep = "_")
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snp[snp=="q_p"]<-"p_q"
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snp_f<-factor(snp,levels=c("p_p", "p_q", "q_q"))
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a<-length(snp)*2
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b<-length(snp)
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p<-(length(al1[al1=="p"])+length(al2[al2=="p"]))/a
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q<-(length(al1[al1=="q"])+length(al2[al2=="q"]))/a
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al_dist<-round(rbind(cbind(p*a,q*a),cbind(p*100,q*100)),1)
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al_names<-levels(factor(x))
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p_p<-round(p^2*b,3)
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p_q<-round(2*p*q*b,3)
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q_q<-round(q^2*b,3)
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hwe<-data.frame(obs=summary(snp_f),exp=rbind(p_p, p_q, q_q))
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hwe$dev<-hwe$obs-hwe$exp
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hwe$chi<-hwe$dev^2/hwe$exp
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snp_obs<-round(rbind(summary(snp_f),summary(snp_f)/length(snp_f)*100),1)
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snp_exp<-round(rbind(hwe$exp,hwe$exp/b*100),1)
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gen_names<-c(
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paste(levels(factor(x))[1],levels(factor(x))[1],sep="_"),
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paste(levels(factor(x))[1],levels(factor(x))[2],sep="_"),
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paste(levels(factor(x))[2],levels(factor(x))[2],sep="_"))
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chi<-sum(hwe$chi,na.rm = TRUE)
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p_v<-pchisq(chi, df=df, lower.tail=FALSE)
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}
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else if(all==3){
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df=3
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## Triallellic system, df=3
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al1<-factor(x,labels=c("p","q","r"))
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al2<-factor(y,labels=c("p","q","r"))
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snp<-paste(al1,al2,sep = "_")
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snp[snp=="r_p"]<-"p_r"
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snp[snp=="r_q"]<-"q_r"
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snp[snp=="q_p"]<-"p_q"
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snp_f<-factor(snp,levels=c("p_p", "p_q", "q_q","p_r","q_r", "r_r"))
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a<-length(snp)*2
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b<-length(snp)
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p<-(length(al1[al1=="p"])+length(al2[al2=="p"]))/a
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q<-(length(al1[al1=="q"])+length(al2[al2=="q"]))/a
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r<-(length(al1[al1=="r"])+length(al2[al2=="r"]))/a
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al_dist<-round(rbind(cbind(p*a,q*a,r*a),cbind(p*100,q*100,r*100)),1)
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al_names<-levels(factor(x))
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p_p<-round(p^2*b,3)
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p_q<-round(2*p*q*b,3)
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q_q<-round(q^2*b,3)
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p_r<-round(2*r*p*b,3)
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q_r<-round(2*q*r*b,3)
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r_r<-round(r^2*b,3)
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hwe<-data.frame(obs=summary(snp_f),exp=rbind(p_p, p_q, q_q, p_r, q_r, r_r))
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hwe$dev<-hwe$obs-hwe$exp
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hwe$chi<-hwe$dev^2/hwe$exp
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snp_obs<-round(rbind(summary(snp_f),summary(snp_f)/length(snp_f)*100),1)
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snp_exp<-round(rbind(hwe$exp,hwe$exp/b*100),1)
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gen_names<-c(
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paste(levels(factor(x))[1],levels(factor(x))[1],sep="_"),
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paste(levels(factor(x))[1],levels(factor(x))[2],sep="_"),
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paste(levels(factor(x))[2],levels(factor(x))[2],sep="_"),
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paste(levels(factor(x))[1],levels(factor(x))[3],sep="_"),
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paste(levels(factor(x))[2],levels(factor(x))[3],sep="_"),
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paste(levels(factor(x))[3],levels(factor(x))[3],sep="_"))
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chi<-sum(hwe$chi,na.rm = TRUE)
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p_v<-pchisq(chi, df=df, lower.tail=FALSE)
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}
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else if (!any(all==c(2,3))){stop("This formula only works for bi- or triallellic systems")}
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else {stop("There was an unknown error")}
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colnames(al_dist)<-al_names
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colnames(snp_obs)<-gen_names
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colnames(snp_exp)<-gen_names
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rn<-c("N","%")
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rownames(al_dist)<-rn
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rownames(snp_obs)<-rn
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rownames(snp_exp)<-rn
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int<-ifelse(p_v<=0.05,"The null-hypothesis of difference from the HWE can be confirmed","The null-hypothesis of difference from the HWE can be rejected")
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t1<-"Chi-square test for Hardy-Weinberg equillibrium for a bi- or triallellic system. Read more: http://www.husdyr.kvl.dk/htm/kc/popgen/genetics/2/2.htm"
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list<-list(info=t1,n.total=b,allele.dist=al_dist,observed.dist=snp_obs,expected.dist=snp_exp,chi.value=chi,p.value=p_v,df=df,interpretation=int)
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return(list)
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}
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