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Copy pathCWDPRNP_ver0.R
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CWDPRNP_ver0.R
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############PRNP Functions##############
####Checks install packages####
CheckCRANPackages <- function(packages, repos="http://cran.r-project.org",
depend=c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")) {
for(p in packages) {
pckg=try( require(p, character.only=TRUE) )
if(!pckg) {
install.packages(p, repos=repos, dependencies=depend)
}
require(p, character.only=TRUE)
}
}
CheckBioconductorPackages <- function(packages,
depend=c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")) {
for(p in packages) {
pckg=try( require(p, character.only=TRUE) )
if(!pckg) {
source("https://bioconductor.org/biocLite.R")
biocLite(p, dependencies=depend)
}
require(p, character.only=TRUE)
}
}
####Necessary Background Functions####
list.DNAStringSet<-function(x){
Biostrings::DNAStringSet(unlist(x, use.names=T),use.names=T)
}
list.contig<-function(x){
DNAString(as.character(ConsensusSequence(x, noConsensusChar = "S")))
}
align.method<-function(x, method){
if(method=="DECIPHER"){
align<-DECIPHER::AlignSeqs(x)
return(align)
}
if(method=="ClustalW"){
align<-msa(x, method=c("ClustalW"))
return(align)
}
if(method=="ClustalOmega"){
align<-msa(x, method=c("ClustalOmega"))
return(align)
}
if(method=="Muscle"){
align<-msa(x, method=c("Muscle"))
return(align)
}
}
########
####Load Reference Sequence####
RefSeq<-function(x,accession){
if(x=="CECA"){
elk<-ape::read.GenBank("AF016228")
ape::write.dna(elk, file="CECAprion.fasta", format="fasta", nbcol=10, colsep="")
elk.prion<-Biostrings::readDNAStringSet("CECAprion.fasta")
elk.prion<-unlist(elk.prion)
elk.prion<-as.character(elk.prion)
elk.prion<-paste(elk.prion, sep="", collapse="")
elk.prion<-Biostrings::DNAString(elk.prion)
return(elk.prion)}
if(x=="ODVI"){
wtd<-read.GenBank("AY275712")
write.dna(wtd, file="ODVIprion.fasta", format="fasta",nbcol=10, colsep="")
wtd.prion<-readDNAStringSet("ODVIprion.fasta")
wtd.prion<-unlist(wtd.prion)
wtd.prion<-as.character(wtd.prion)
wtd.prion<-paste(wtd.prion, sep="", collapse="")
wtd.prion<-DNAString(wtd.prion)
return(wtd.prion)
}
if(x=="ODHE"){
mule<-read.GenBank("U25965")
write.dna(mule, file="ODHEprion.fasta", format="fasta",nbcol=10, colsep="")
mule.prion<-readDNAStringSet("ODHEprion.fasta")
mule.prion<-unlist(mule.prion)
mule.prion<-as.character(mule.prion)
mule.prion<-paste(mule.prion, sep="", collapse="")
mule.prion<-DNAString(mule.prion)
return(mule.prion)
}
if(x=="RATA"){
rein<-read.GenBank("AY639093")
write.dna(rein, file="RATAprion.fasta", format="fasta", nbcol=10, colsep="")
rein.prion<-readDNAStringSet("RATAprion.fasta")
rein.prion<-unlist(rein.prion)
rein.prion<-as.character(rein.prion)
rein.prion<-paste(rein.prion, sep="", collapse="")
rein.prion<-DNAString(rein.prion)
return(rein.prion)
}
if(x==c("other")){
y<-accession
ref<-read.GenBank(y)
write.dna(ref, file="refprion.fasta", format="fasta",nbcol=10, colsep="")
ref.prion<-readDNAStringSet("refprion.fasta")
ref.prion<-unlist(ref.prion)
ref.prion<-as.character(ref.prion)
ref.prion<-paste(ref.prion, sep="", collapse="")
ref.prion<-DNAString(ref.prion)
return(ref.prion)
}
}
####
#########Call Bases
CallBases<-function(flab, rlab, label){
temp<-list.files(pattern=flab)
temp2<-list.files(pattern=rlab)
sub<-gsub(label, "", temp2)
names(temp)<-names(temp2)<-sub
forward<-lapply(temp, sangerseqR::readsangerseq)
forward<-lapply(forward, sangerseqR::makeBaseCalls)
reverse<-lapply(temp2, sangerseqR::readsangerseq)
reverse<-lapply(reverse, sangerseqR::makeBaseCalls)
list<-list(forward,reverse)
return(list)
}
####
###############Write Chromatograms
Chrom<-function(forward,reverse){
key<-names(forward)
pdf1<-paste(key, "F.pdf", sep="")
for(i in 1:length(forward)){
sangerseqR::chromatogram(forward[[i]],showcalls = c("both"), filename=pdf1[[i]], showhets=T)
}
pdf2<-paste(key, "R.pdf", sep="")
for(i in 1:length(reverse)){
sangerseqR::chromatogram(reverse[[i]], showcalls = c("both"), filename=pdf2[[i]], showhets=T)
}
}
##################
####Alignments####
Align<-function(ref, forward, reverse, method){
ref<-cbind(c("Ref"), as.character(ref))
key<-names(forward)
key1<-c(key, "Ref")
f1<-list()
for(i in 1:length(forward)){
f1[[i]]<-as.character(unlist(forward[[i]]@primarySeq))
}
f1<-cbind(key,as.matrix(unlist(f1)))
colnames(f1)<-c("ID", "Sequence")
f1<-rbind(f1, as.character(ref))
f1prim<-list()
for(i in 1:length(f1[,2])){
f1prim[[i]]<-Biostrings::DNAString(f1[i,2])
}
names(f1prim)<-f1[,1]
f1align<-list.DNAStringSet(f1prim)
f1align<-align.method(f1align, method)
f1trim<-as.matrix(f1align)
f1trim<-f1trim[,-which(f1trim["Ref",]=="-")]
f1trim<-as.data.frame(f1trim)
f1trim<-f1trim[match(key1, rownames(f1trim)),]
f1trim<-data.frame(lapply(f1trim, as.character), stringsAsFactors=F)
f2<-list()
for(i in 1:length(forward)){
f2[[i]]<-as.character(unlist(forward[[i]]@secondarySeq))
}
f2<-cbind(key, as.matrix(unlist(f2)))
colnames(f2)<-c("ID","Sequence")
f2<-rbind(f2, as.character(ref))
f2prim<-list()
for(i in 1:length(f2[,2])){
f2prim[[i]]<-Biostrings::DNAString(f2[i,2])
}
names(f2prim)<-f2[,1]
f2align<-list.DNAStringSet(f2prim)
f2align<-align.method(f2align, method)
f2trim<-as.matrix(f2align)
f2trim<-f2trim[,-which(f2trim["Ref",]=="-")]
f2trim<-as.data.frame(f2trim)
f2trim<-f2trim[match(key1, rownames(f2trim)),]
f2trim<-data.frame(lapply(f2trim, as.character), stringsAsFactors=F)
comp1<-list()
for(i in 1:length(reverse)){
comp1[[i]]<-reverse[[i]]@primarySeq
}
comp1<-Biostrings::DNAStringSet(comp1)
comp1<-Biostrings::reverseComplement(comp1)
comp1<-cbind(key, as.character(comp1))
r1<-rbind(comp1, as.character(ref))
colnames(r1)<-c("ID","Sequence")
r1prim<-list()
for(i in 1:length(r1[,2])){
r1prim[[i]]<-Biostrings::DNAString(r1[i,2])
}
names(r1prim)<-r1[,1]
r1align<-list.DNAStringSet(r1prim)
r1align<-align.method(r1align, method)
r1trim<-as.matrix(r1align)
r1trim<-r1trim[,-which(r1trim["Ref",]=="-")]
r1trim<-as.data.frame(r1trim)
r1trim<-r1trim[match(key1, rownames(r1trim)),]
r1trim<-data.frame(lapply(r1trim, as.character), stringsAsFactors=F)
comp2<-list()
for(i in 1:length(reverse)){
comp2[[i]]<-reverse[[i]]@secondarySeq
}
comp2<-Biostrings::DNAStringSet(comp2)
comp2<-Biostrings::reverseComplement(comp2)
comp2<-cbind(key, as.character(comp2))
r2<-rbind(comp2, as.character(ref))
colnames(r2)<-c("ID","Sequence")
r2prim<-list()
for(i in 1:length(r2[,2])){
r2prim[[i]]<-Biostrings::DNAString(r2[i,2])
}
names(r2prim)<-r2[,1]
r2align<-list.DNAStringSet(r2prim)
r2align<-align.method(r2align, method)
r2trim<-as.matrix(r2align)
r2trim<-r2trim[,-which(r2trim["Ref",]=="-")]
r2trim<-as.data.frame(r2trim)
r2trim<-r2trim[match(key1, rownames(r2trim)),]
r2trim<-data.frame(lapply(r2trim, as.character), stringsAsFactors=F)
rownames(f1trim)<-rownames(f2trim)<-rownames(r1trim)<-rownames(r2trim)<-key1
list<-list(f1trim, f2trim, r1trim, r2trim)
return(list)
}
##################
####Align Raw####
Poly<-function(poly, align, ref){
if(poly==F){
fallele1<-align[[1]]
fallele2<-align[[2]]
rallele1<-align[[3]]
rallele2<-align[[4]]
key<-rownames(fallele1)
a1lab<-paste(key, "_a1", sep="")
a2lab<-paste(key, "_a2", sep="")
rownames(fallele1)<-a1lab
rownames(fallele2)<-a2lab
rownames(rallele1)<-a1lab
rownames(rallele2)<-a2lab
newf<-rbind(fallele1, fallele2)
newr<-rbind(rallele1, rallele2)
newf<-newf[!rownames(newf) %in% c("Ref_a1", "Ref_a2"),]
newr<-newr[!rownames(newr) %in% c("Ref_a1", "Ref_a2"),]
newf<-newf[order(row.names(newf)),]
newr<-newr[order(row.names(newr)),]
ref1<-t(as.matrix(strsplit(as.character(ref), split="")[[1]]))
rownames(ref1)<-c("Ref")
newf<-rbind(newf, ref1)
newr<-rbind(newr, ref1)
colnames(newf)<-colnames(newr)<-c(1:ncol(newr))
new<-list(newf, newr)
return(new)
}
if(poly==T){
fallele1<-align[[1]]
fallele2<-align[[2]]
rallele1<-align[[3]]
rallele2<-align[[4]]
key<-rownames(fallele1)
a1lab<-paste(key, "_a1", sep="")
a2lab<-paste(key, "_a2", sep="")
rownames(fallele1)<-a1lab
rownames(fallele2)<-a2lab
rownames(rallele1)<-a1lab
rownames(rallele2)<-a2lab
newf<-rbind(fallele1, fallele2)
newr<-rbind(rallele1, rallele2)
newf<-newf[!rownames(newf) %in% c("Ref_a1", "Ref_a2"),]
newr<-newr[!rownames(newr) %in% c("Ref_a1", "Ref_a2"),]
newf<-newf[order(row.names(newf)),]
newr<-newr[order(row.names(newr)),]
ref1<-t(as.matrix(strsplit(as.character(ref), split="")[[1]]))
rownames(ref1)<-c("Ref")
newf<-rbind(newf, ref1)
newr<-rbind(newr, ref1)
colnames(newf)<-colnames(newr)<-c(1:ncol(newr))
new1<-matrix(0,nrow=1,ncol=ncol(newf))
for(i in 1:ncol(newf)){
new1[i]<-length(unique(newf[,i]))
}
new2<-matrix(0,nrow=1,ncol=ncol(newr))
for(i in 1:ncol(newr)){
new2[i]<-length(unique(newr[,i]))
}
rownames(new1)<-rownames(new2)<-c("Poly")
colnames(new1)<-colnames(new2)<-colnames(newf)
newf<-rbind(newf,new1)
newr<-rbind(newr,new2)
new<-list(newf,newr)
return(new)
}
}
######################################
####ExtractSNPs####
ExtractSNPs<-function(align){
alignf<-align[[1]]
alignr<-align[[2]]
alignf<-as.data.frame(t(alignf))
Polyf<-as.numeric(alignf$Poly)
alignf<-alignf[,-c(ncol(alignf))]
alignf$Poly<-Polyf
alignf<-alignf[alignf$Poly>1,]
alignf<-t(alignf)
alignr<-as.data.frame(t(alignr))
Polyr<-as.numeric(alignr$Poly)
alignr<-alignr[,-c(ncol(alignr))]
alignr$Poly<-Polyr
alignr<-alignr[alignr$Poly>1,]
alignr<-t(alignr)
polyf<-as.numeric(colnames(alignf))
polyr<-as.numeric(colnames(alignr))
polyf1<-which(polyf %in% polyr)
polyr1<-which(polyr %in% polyf)
polyf<-alignf[,polyf1]
polyr<-alignr[,polyr1]
ref<-t(as.matrix(polyr["Ref",]))
rownames(ref)<-c("Ref")
polyf<-polyf[!rownames(polyf) %in% c("Ref", "Poly"),]
polyr<-polyr[!rownames(polyr) %in% c("Ref", "Poly"),]
a1lab<-paste(rownames(polyf), "F", sep="")
a2lab<-paste(rownames(polyr), "R", sep="")
key<-c(a1lab,a2lab)
polyfull<-rbind(polyf,polyr)
rownames(polyfull)<-key
polyfull<-polyfull[order(rownames(polyfull)),]
polyfull<-rbind(polyfull,ref)
SNPs<-list(polyfull,polyf, polyr)
return(SNPs)
}
################################
####Nucleotide Table####
NucTab<-function(x, align, nuc){
if(x=="CECA"){
PRNPlabels<-c(394)
key<-rownames(align[[1]])
align2<-list()
for(i in 1:length(PRNPlabels)){
align2[[i]]<-cbind(align[[1]][,PRNPlabels[i]], align[[2]][,PRNPlabels[i]], align[[3]][,PRNPlabels[i]], align[[4]][,PRNPlabels[i]])
}
nuc394f<-apply(align2[[1]][,c(1,2)], 1, paste, collapse="/")
nuc394r<-apply(align2[[1]][,c(3,4)], 1, paste, collapse="/")
nuc394geno<-matrix(0, nrow=NROW(nuc394f), ncol=1, dimnames=list(c(rownames(align2[[1]])), c("Genotype")))
nuc394geno[,1]<-ifelse((nuc394f=="A/A")&(nuc394r=="A/A"),c("A/A"),nuc394geno)
nuc394geno[,1]<-ifelse(((nuc394f=="A/T")|(nuc394f=="T/A"))&((nuc394r=="A/T")|(nuc394r=="T/A")), c("A/T"),nuc394geno)
nuc394geno[,1]<-ifelse((nuc394f=="T/T")&(nuc394r=="T/T"), c("T/T"), nuc394geno)
nuc394geno[,1]<-ifelse(nuc394geno==0, c("ERROR"), nuc394geno)
colnames(nuc394geno)<-c("nuc394")
rownames(nuc394geno)<-key
return(nuc394geno)
}
if(x=="ODVI"){
PRNPlabels<-c(285, 286, 347)
key<-rownames(align[[1]])
align2<-list()
for(i in 1:length(PRNPlabels)){
align2[[i]]<-cbind(align[[1]][,PRNPlabels[i]], align[[2]][,PRNPlabels[i]], align[[3]][,PRNPlabels[i]], align[[4]][,PRNPlabels[i]])
}
nuc285<-align2[[1]]
nuc285f<-apply(nuc285[,c(1,2)], 1, paste, collapse="/")
nuc285r<-apply(nuc285[,c(3,4)], 1, paste, collapse="/")
nuc285geno<-matrix(0, nrow=NROW(nuc285f), ncol=1, dimnames=list(c(rownames(nuc285)), c("Genotype")))
nuc285geno[,1]<-ifelse((nuc285f=="A/A")&(nuc285r=="A/A"),c("A/A"), nuc285geno)
nuc285geno[,1]<-ifelse(((nuc285f=="A/C")|(nuc285f=="C/A"))&((nuc285r=="A/C")|(nuc285r=="C/A")), c("A/C"),nuc285geno)
nuc285geno[,1]<-ifelse((nuc285f=="C/C")&(nuc285r=="C/C"), c("C/C"), nuc285geno)
nuc285geno[,1]<-ifelse(nuc285geno==0, c("ERROR"), nuc285geno)
nuc286<-align2[[2]]
nuc286f<-apply(nuc286[,c(1,2)], 1, paste, collapse="/")
nuc286r<-apply(nuc286[,c(3,4)], 1, paste, collapse="/")
nuc286geno<-matrix(0, nrow=NROW(nuc286f), ncol=1, dimnames=list(c(rownames(nuc286)), c("Genotype")))
nuc286geno[,1]<-ifelse((nuc286f=="G/G")&(nuc286r=="G/G"),c("G/G"), nuc286geno)
nuc286geno[,1]<-ifelse(((nuc286f=="G/A")|(nuc286f=="A/G"))&((nuc286r=="G/A")|(nuc286r=="A/G")), c("G/A"),nuc286geno)
nuc286geno[,1]<-ifelse((nuc286f=="A/A")&(nuc286r=="A/A"), c("A/A"), nuc286geno)
nuc286geno[,1]<-ifelse(nuc286geno==0, c("ERROR"), nuc286geno)
nuc347<-align2[[3]]
nuc347f<-apply(nuc347[,c(1,2)], 1, paste, collapse="/")
nuc347r<-apply(nuc347[,c(3,4)], 1, paste, collapse="/")
nuc347geno<-matrix(0, nrow=NROW(nuc347f), ncol=1, dimnames=list(c(rownames(nuc347)), c("Genotype")))
nuc347geno[,1]<-ifelse((nuc347f=="C/C")&(nuc347r=="C/C"),c("C/C"), nuc347geno)
nuc347geno[,1]<-ifelse(((nuc347f=="C/G")|(nuc347f=="G/C"))&((nuc347r=="C/G")|(nuc347r=="G/C")), c("C/G"),nuc347geno)
nuc347geno[,1]<-ifelse((nuc347f=="G/G")&(nuc347r=="G/G"), c("G/G"), nuc347geno)
nuc347geno[,1]<-ifelse(nuc347geno==0, c("ERROR"), nuc347geno)
ODVIgeno<-cbind(nuc285geno, nuc286geno, nuc347geno)
colnames(ODVIgeno)<-c("nuc285", "nuc286", "nuc347")
rownames(ODVIgeno)<-key
return(ODVIgeno)
}
if(x=="ODHE"){
PRNPlabels<-c(674)
key<-rownames(align[[1]])
align2<-list()
for(i in 1:length(PRNPlabels)){
align2[[i]]<-cbind(align[[1]][,PRNPlabels[i]], align[[2]][,PRNPlabels[i]], align[[3]][,PRNPlabels[i]], align[[4]][,PRNPlabels[i]])
}
nuc674f<-apply(align2[[1]][,c(1,2)], 1, paste, collapse="/")
nuc674r<-apply(align2[[1]][,c(3,4)], 1, paste, collapse="/")
nuc674geno<-matrix(0, nrow=NROW(nuc674f), ncol=1, dimnames=list(c(rownames(align2[[1]])), c("Genotype")))
nuc674geno[,1]<-ifelse((nuc674f=="C/C")&(nuc674r=="C/C"),c("C/C"),nuc674geno)
nuc674geno[,1]<-ifelse(((nuc674f=="C/T")|(nuc674f=="T/C"))&((nuc674r=="C/T")|(nuc674r=="T/C")), c("C/T"),nuc674geno)
nuc674geno[,1]<-ifelse((nuc674f=="T/T")&(nuc674r=="T/T"), c("T/T"), nuc674geno)
nuc674geno[,1]<-ifelse(nuc674geno==0, c("ERROR"), nuc674geno)
colnames(nuc674geno)<-c("nuc674")
rownames(nuc674geno)<-key
return(nuc674geno)
}
if(x=="other"){
PRNPlabels<-nuc
key<-rownames(align[[1]])
align2<-list()
for(i in 1:length(PRNPlabels)){
align2[[i]]<-cbind(align[[1]][,PRNPlabels[i]], align[[2]][,PRNPlabels[i]], align[[3]][,PRNPlabels[i]], align[[4]][,PRNPlabels[i]])
}
for(i in 1:length(align2)){
align2[[i]]<-ifelse(align2[[i]]!="A"&align2[[i]]!="G"&align2[[i]]!="C"&align2[[i]]!="T","-",align2[[i]])
}
NucMat<-c(1,5,6,7,"-",5,2,8,9,"-",6,8,3,10,"-",7,9,10,4,"-","-","-","-","-","-")
NucMat<-matrix(NucMat, nrow=5, ncol=5)
rownames(NucMat)<-colnames(NucMat)<-c("A","T","C","G","-")
GenList<-list()
for(i in 1:length(align2)){
GenList[[i]]<-matrix(0, nrow=NROW(align2[[1]]), ncol=2, dimnames=list(c(rownames(align2)), c("GenF","GenR")))
}
error<-list()
for(i in 1:length(align2)){
error[[i]]<-matrix(0, nrow=NROW(align2[[1]]), ncol=1)
}
for(i in 1:length(GenList)){
for(j in 1:nrow(GenList[[1]])){
GenList[[i]][j,1]<-NucMat[align2[[i]][j,1],align2[[i]][j,2]]
GenList[[i]][j,2]<-NucMat[align2[[i]][j,3],align2[[i]][j,4]]
error[[i]][j,1]<-ifelse(GenList[[i]][j,1]==GenList[[i]][j,2],GenList[[i]][j,1], "Error")
error[[i]][j,1]<-ifelse(GenList[[i]][j,1]=="-","Error",error[[i]][j,1])
GenList[[i]]<-cbind(GenList[[i]],error[[i]])
GenList[[i]]<-cbind(GenList[[i]][,c(1,2)],GenList[[i]][,ncol(GenList[[i]])])
}
}
list<-list()
for(i in 1:length(align2)){
list[[i]]<-matrix("-", nrow=NROW(align2[[i]]), ncol=1, dimnames=list(c(rownames(align2[[i]])), c("Genotype")))
list[[i]][,1]<-ifelse(GenList[[i]][,3]=="1", "A/A", list[[i]][,1])
list[[i]][,1]<-ifelse(GenList[[i]][,3]=="2", "T/T", list[[i]][,1])
list[[i]][,1]<-ifelse(GenList[[i]][,3]=="3", "C/C", list[[i]][,1])
list[[i]][,1]<-ifelse(GenList[[i]][,3]=="4", "G/G", list[[i]][,1])
list[[i]][,1]<-ifelse(GenList[[i]][,3]=="5", "A/T", list[[i]][,1])
list[[i]][,1]<-ifelse(GenList[[i]][,3]=="6", "A/C", list[[i]][,1])
list[[i]][,1]<-ifelse(GenList[[i]][,3]=="7", "A/G", list[[i]][,1])
list[[i]][,1]<-ifelse(GenList[[i]][,3]=="8", "T/C", list[[i]][,1])
list[[i]][,1]<-ifelse(GenList[[i]][,3]=="9", "T/G", list[[i]][,1])
list[[i]][,1]<-ifelse(GenList[[i]][,3]=="10", "C/G", list[[i]][,1])
list[[i]][,1]<-ifelse(GenList[[i]][,3]=="Error", "Error", list[[i]][,1])
}
names(list)<-PRNPlabels
NucTab<-matrix(0, nrow=NROW(list[[1]]), ncol=length(list), dimnames=list(c(rownames(list[[1]])), c(PRNPlabels)))
for(i in 1:length(list)){
for(j in 1:nrow(list[[1]])){
NucTab[j,i]<-list[[i]][j,1]
}
}
rownames(NucTab)<-key
return(NucTab)
}
}
####################################
####Codon Table########
CodTab<-function(x, Tab, align){
if(x=="CECA"){
NucTab<-Tab
CECAcodon<-matrix(0, nrow=NROW(NucTab), ncol=1, dimnames=list(c(rownames(NucTab)), c("cod132")))
CECAcodon[,1]<-ifelse(NucTab[,c("nuc394")]=="A/A", "M/M", CECAcodon[,1])
CECAcodon[,1]<-ifelse(NucTab[,c("nuc394")]=="A/T", "M/L", CECAcodon[,1])
CECAcodon[,1]<-ifelse(NucTab[,c("nuc394")]=="T/T", "L/L", CECAcodon[,1])
CECAcodon[,1]<-ifelse(NucTab[,c("nuc394")]=="ERROR", "ERROR", CECAcodon[,1])
return(CECAcodon)
}
if(x=="ODVI"){
NucTab<-Tab
ODVIcodon<-matrix(0, nrow=NROW(NucTab), ncol=3, dimnames=list(c(rownames(NucTab)), c("cod95", "cod96", "cod116")))
ODVIcodon[,1]<-ifelse(NucTab[,c("nuc285")]=="A/A", "Q/Q", ODVIcodon[,1])
ODVIcodon[,1]<-ifelse(NucTab[,c("nuc285")]=="A/C", "Q/H", ODVIcodon[,1])
ODVIcodon[,1]<-ifelse(NucTab[,c("nuc285")]=="C/C", "H/H", ODVIcodon[,1])
ODVIcodon[,1]<-ifelse(NucTab[,c("nuc285")]=="ERROR", "ERROR", ODVIcodon[,1])
ODVIcodon[,2]<-ifelse(NucTab[,c("nuc286")]=="G/G", "G/G", ODVIcodon[,2])
ODVIcodon[,2]<-ifelse(NucTab[,c("nuc286")]=="G/A", "G/S", ODVIcodon[,2])
ODVIcodon[,2]<-ifelse(NucTab[,c("nuc286")]=="A/A", "S/S", ODVIcodon[,2])
ODVIcodon[,2]<-ifelse(NucTab[,c("nuc286")]=="ERROR", "ERROR", ODVIcodon[,2])
ODVIcodon[,3]<-ifelse(NucTab[,c("nuc347")]=="C/C", "A/A", ODVIcodon[,3])
ODVIcodon[,3]<-ifelse(NucTab[,c("nuc347")]=="C/G", "A/G", ODVIcodon[,3])
ODVIcodon[,3]<-ifelse(NucTab[,c("nuc347")]=="G/G", "G/G", ODVIcodon[,3])
ODVIcodon[,3]<-ifelse(NucTab[,c("nuc347")]=="ERROR", "ERROR", ODVIcodon[,3])
return(ODVIcodon)
}
if(x=="ODHE"){
NucTab<-Tab
ODHEcodon<-matrix(0, nrow=NROW(NucTab), ncol=1, dimnames=list(c(rownames(NucTab)), c("cod225")))
ODHEcodon[,1]<-ifelse(NucTab[,c("nuc674")]=="C/C", "S/S", ODHEcodon[,1])
ODHEcodon[,1]<-ifelse(NucTab[,c("nuc674")]=="C/T", "S/F", ODHEcodon[,1])
ODHEcodon[,1]<-ifelse(NucTab[,c("nuc674")]=="T/T", "F/F", ODHEcodon[,1])
ODHEcodon[,1]<-ifelse(NucTab[,c("nuc674")]=="ERROR", "ERROR", ODHEcodon[,1])
return(ODHEcodon)
}
if(x=="other"){
AATab<-align
colnames(AATab[[1]])<-colnames(AATab[[2]])<-colnames(AATab[[3]])<-colnames(AATab[[4]])<-c(1:ncol(AATab[[1]]))
PRNPlabels<-colnames(Tab)
Nuc<-as.numeric(PRNPlabels)
Cod<-vector("integer", length(Nuc))
for(i in 1:length(Cod)){
Cod[i]<-Nuc[i]/3
}
Pos<-vector("integer", length(Cod))
Pos<-ifelse(Cod-trunc(Cod)>0 & Cod-trunc(Cod)<0.34,1,Pos)
Pos<-ifelse(Cod-trunc(Cod)>0.34 & Cod-trunc(Cod)<0.67,2,Pos)
Pos<-ifelse(Cod-trunc(Cod)==0,3, Pos)
Cod<-ceiling(Cod)
CodList<-list()
for(i in 1:length(Nuc)){
CodList[[i]]<-vector("integer",3)
}
for(i in 1:length(Nuc)){
if(Pos[i]==3){
CodList[[i]][1]<-Nuc[i]-2
CodList[[i]][2]<-Nuc[i]-1
CodList[[i]][3]<-Nuc[i]
}
if(Pos[i]==2){
CodList[[i]][1]<-Nuc[i]-1
CodList[[i]][2]<-Nuc[i]
CodList[[i]][3]<-Nuc[i]+1
}
if(Pos[i]==1){
CodList[[i]][1]<-Nuc[i]
CodList[[i]][2]<-Nuc[i]+1
CodList[[i]][3]<-Nuc[i]+2
}
}
NucList<-list()
for(i in 1:length(align)){
NucList[[i]]<-cbind(align[[i]][,unlist(CodList)])
colnames(NucList[[i]])<-unlist(CodList)
}
Nuc1<-list()
for(i in 1:length(align)){
Nuc1[[i]]<-align[[i]][,Nuc]
Nuc1[[i]]<-as.matrix(Nuc1[[i]])
colnames(Nuc1[[i]])<-Nuc
}
NucList<-list(Cod, Nuc1, NucList)
Key<-NucList[[1]]
codons<-NucList[[3]]
for1<-codons[[1]]
for1<-as.matrix(for1)
for1<-ifelse(for1!="A"&for1!="G"&for1!="C"&for1!="T","-",for1)
er1<-for1[for1[,1]=="-",]
er2<-for1[for1[,2]=="-",]
er3<-for1[for1[,3]=="-",]
er<-c(rownames(er1),rownames(er2),rownames(er3))
er<-unique(er)
for1<-for1[!rownames(for1)%in%er,]
DNA1<-list()
for(i in 1:nrow(for1)){
DNA1[i]<-paste(for1[i,], collapse="")
}
names(DNA1)<-rownames(for1)
for(i in 1:length(DNA1)){
DNA1[[i]]<-DNAString(DNA1[[i]])
}
AA1<-list()
for(i in 1:length(DNA1)){
AA1[[i]]<-Biostrings::translate(DNA1[[i]])
AA1[[i]]<-as.character(AA1[[i]])
AA1[[i]]<-strsplit(AA1[[i]], split="")
}
AA1<-t(matrix(as.vector(unlist(AA1)),nrow=length(Cod),ncol=length(DNA1), dimnames=list(round(Cod),c(names(DNA1)))))
for2<-codons[[2]]
for2<-as.matrix(for2)
for2<-ifelse(for2!="A"&for2!="G"&for2!="C"&for2!="T","-",for2)
er1<-for2[for2[,1]=="-",]
er2<-for2[for2[,2]=="-",]
er3<-for2[for2[,3]=="-",]
er<-c(rownames(er1),rownames(er2),rownames(er3))
er<-unique(er)
for2<-for2[!rownames(for2)%in%er,]
DNA2<-list()
for(i in 1:nrow(for2)){
DNA2[i]<-paste(for2[i,], collapse="")
}
names(DNA2)<-rownames(for2)
for(i in 1:length(DNA2)){
DNA2[[i]]<-DNAString(DNA2[[i]])
}
AA2<-list()
for(i in 1:length(DNA2)){
AA2[[i]]<-Biostrings::translate(DNA2[[i]])
AA2[[i]]<-as.character(AA2[[i]])
AA2[[i]]<-strsplit(AA2[[i]], split="")
}
AA2<-t(matrix(as.vector(unlist(AA2)),nrow=length(Cod),ncol=length(DNA2), dimnames=list(round(Cod),c(names(DNA2)))))
rev1<-codons[[3]]
rev1<-as.matrix(rev1)
rev1<-ifelse(rev1!="A"&rev1!="G"&rev1!="C"&rev1!="T","-",rev1)
er1<-rev1[rev1[,1]=="-",]
er2<-rev1[rev1[,2]=="-",]
er3<-rev1[rev1[,3]=="-",]
er<-c(rownames(er1),rownames(er2),rownames(er3))
er<-unique(er)
rev1<-rev1[!rownames(rev1)%in%er,]
DNA3<-list()
for(i in 1:nrow(rev1)){
DNA3[i]<-paste(rev1[i,], collapse="")
}
names(DNA3)<-rownames(rev1)
for(i in 1:length(DNA3)){
DNA3[[i]]<-DNAString(DNA3[[i]])
}
AA3<-list()
for(i in 1:length(DNA3)){
AA3[[i]]<-Biostrings::translate(DNA3[[i]])
AA3[[i]]<-as.character(AA3[[i]])
AA3[[i]]<-strsplit(AA3[[i]], split="")
}
AA3<-t(matrix(as.vector(unlist(AA3)),nrow=length(Cod),ncol=length(DNA3), dimnames=list(round(Cod),c(names(DNA3)))))
rev2<-codons[[4]]
rev2<-as.matrix(rev2)
rev2<-ifelse(rev2!="A"&rev2!="G"&rev2!="C"&rev2!="T","-",rev2)
er1<-rev2[rev2[,1]=="-",]
er2<-rev2[rev2[,2]=="-",]
er3<-rev2[rev2[,3]=="-",]
er<-c(rownames(er1),rownames(er2),rownames(er3))
er<-unique(er)
rev2<-rev2[!rownames(rev2)%in%er,]
DNA4<-list()
for(i in 1:nrow(rev2)){
DNA4[i]<-paste(rev2[i,], collapse="")
}
names(DNA4)<-rownames(rev2)
for(i in 1:length(DNA4)){
DNA4[[i]]<-DNAString(DNA4[[i]])
}
AA4<-list()
for(i in 1:length(DNA4)){
AA4[[i]]<-Biostrings::translate(DNA4[[i]])
AA4[[i]]<-as.character(AA4[[i]])
AA4[[i]]<-strsplit(AA4[[i]], split="")
}
AA4<-t(matrix(as.vector(unlist(AA4)),nrow=length(Cod),ncol=length(DNA4), dimnames=list(round(Cod),c(names(DNA4)))))
AAlist<-list(AA1,AA2,AA3,AA4)
n1<-rownames(AAlist[[1]])
n2<-rownames(AAlist[[2]])
n3<-rownames(AAlist[[3]])
n4<-rownames(AAlist[[4]])
n<-n1[n1%in%n2]
n<-n[n%in%n3]
n<-n[n%in%n4]
for(i in 1:length(AAlist)){
AAlist[[i]]<-AAlist[[i]][n,]
}
PRNPlabels<-as.character(Cod)
AATab<-AAlist
for(i in 1:length(AATab)){
AATab[[i]]<-as.matrix(AATab[[i]])
colnames(AATab[[i]])<-PRNPlabels
}
AAlist<-list()
for(i in 1:length(PRNPlabels)){
AAlist[[i]]<-cbind(AATab[[1]][,PRNPlabels[i]],AATab[[2]][,PRNPlabels[i]], AATab [[3]][,PRNPlabels[i]], AATab[[4]][,PRNPlabels[i]])
}
GenList<-list()
for(i in 1:ncol(AATab[[1]])){
GenList[[i]]<-matrix(0, nrow=NROW(AATab[[1]]), ncol=4)
}
for(i in 1:length(GenList)){
for(j in 1:ncol(GenList[[1]])){
GenList[[i]][,j]<-AATab[[j]][,i]
}
}
GenList1<-list()
for(i in 1:length(GenList)){
GenList1[[i]]<-matrix(0, nrow=NROW(GenList[[1]]), ncol=2)
}
for(i in 1:length(GenList1)){
for(j in 1:nrow(GenList[[1]])){
GenList1[[i]][j,1]<-paste(min(GenList[[i]][j,1:2]), max(GenList[[i]][j,1:2]), sep="/")
GenList1[[i]][j,2]<-paste(min(GenList[[i]][j,3:4]), max(GenList[[i]][j,3:4]), sep="/")
}
}
AAlist1<-list()
for(i in 1:length(GenList1)){
AAlist1[[i]]<-matrix(0, nrow=NROW(GenList1[[1]]), ncol=1)
}
for(i in 1:length(AAlist1)){
for(j in 1:nrow(GenList1[[1]])){
AAlist1[[i]][,1]<-ifelse(GenList1[[i]][,1]==GenList1[[i]][,2], GenList1[[i]][,1], AAlist1[[i]])
AAlist1[[i]][,1]<-ifelse(GenList1[[i]][,1]!=GenList1[[i]][,2], c("Error"), AAlist1[[i]])
}
}
AATab1<-matrix(0, nrow=NROW(GenList[[1]]), ncol=length(AAlist1), dimnames=list(c(rownames(AATab[[1]])),PRNPlabels))
for(i in 1:nrow(AATab1)){
for(j in 1:ncol(AATab1)){
AATab1[i,j]<-AAlist1[[j]][i]
}
}
return(AATab1)
}
}
##################################
####Prop Tables####
PropTab<-function(Pop, x, CodTab, PopLabels){
if(Pop==F){
if(x=="CECA"){
CodTab<-as.matrix(CodTab[!rownames(CodTab)%in% c("Ref"),])
colnames(CodTab)<-c("cod132")
Cod132<-matrix(0, nrow=1, ncol=4, dimnames=list(c("Count"), c("M/M", "M/L", "L/L", "Total")))
Cod132[,c("M/M")]<-sum(CodTab[,c("cod132")]==c("M/M"))
Cod132[,c("M/L")]<-sum(CodTab[,c("cod132")]==c("M/L"))
Cod132[,c("L/L")]<-sum(CodTab[,c("cod132")]==c("L/L"))
Cod132[,c("Total")]<-sum(Cod132)
prop132<-matrix(0, nrow=1, ncol=3, dimnames=list(c("Prop"), c("M/M", "M/L", "L/L")))
prop132[,c("M/M")]<-Cod132[,c("M/M")]/Cod132[,c("Total")]
prop132[,c("M/L")]<-Cod132[,c("M/L")]/Cod132[,c("Total")]
prop132[,c("L/L")]<-Cod132[,c("L/L")]/Cod132[,c("Total")]
Allele132<-matrix(0, nrow=1, ncol=3, dimnames=list(c("Count"), c("M", "L", "Total")))
Allele132[,c("M")]<-(2*sum(CodTab[,c("cod132")]==c("M/M")))+sum(CodTab[,c("cod132")]==c("M/L"))
Allele132[,c("L")]<-(2*sum(CodTab[,c("cod132")]==c("L/L")))+sum(CodTab[,c("cod132")]==c("M/L"))
Allele132[,c("Total")]<-sum(Allele132)
aprop132<-matrix(0,nrow=1,ncol=2, dimnames=list(c("Prop"), c("M","L")))
aprop132[,c("M")]<-Allele132[,c("M")]/Allele132[,c("Total")]
aprop132[,c("L")]<-Allele132[,c("L")]/Allele132[,c("Total")]
GenProp<-matrix(0, nrow=3,ncol=1, dimnames=list(c("Homozygote Major", "Heterozygote", "Homozygote Minor"), c("cod132")))
GenProp[,c("cod132")]<-t(prop132)
AlleleProp<-matrix(0, nrow=2, ncol=1, dimnames=list(c("Major", "Minor"), c("cod132")))
AlleleProp[,c("cod132")]<-t(aprop132)
GenProp<-list(GenProp, AlleleProp, prop132, aprop132)
names(GenProp)<-c("Genotype","Allele", "Geno132", "Allele132")
return(GenProp)
}
if(x=="ODVI"){
CodTab<-CodTab[!rownames(CodTab)%in% c("Ref"),]
Cod95<-matrix(0, nrow=1, ncol=4, dimnames=list(c("Count"), c("Q/Q", "Q/H", "H/H", "Total")))
Cod95[,c("Q/Q")]<-sum(CodTab[,c("cod95")]==c("Q/Q"))
Cod95[,c("Q/H")]<-sum(CodTab[,c("cod95")]==c("Q/H"))
Cod95[,c("H/H")]<-sum(CodTab[,c("cod95")]==c("H/H"))
Cod95[,c("Total")]<-sum(Cod95)
prop95<-matrix(0, nrow=1, ncol=3, dimnames=list(c("Prop"), c("Q/Q", "Q/H", "H/H")))
prop95[,c("Q/Q")]<-Cod95[,c("Q/Q")]/Cod95[,c("Total")]
prop95[,c("Q/H")]<-Cod95[,c("Q/H")]/Cod95[,c("Total")]
prop95[,c("H/H")]<-Cod95[,c("H/H")]/Cod95[,c("Total")]
Allele95<-matrix(0, nrow=1, ncol=3, dimnames=list(c("Count"), c("Q", "H","Total")))
Allele95[,c("Q")]<-(2*sum(CodTab[,c("cod95")]==c("Q/Q")))+sum(CodTab[,c("cod95")]==c("Q/H"))
Allele95[,c("H")]<-(2*sum(CodTab[,c("cod95")]==c("H/H")))+sum(CodTab[,c("cod95")]==c("Q/H"))
Allele95[,c("Total")]<-sum(Allele95)
aprop95<-matrix(0,nrow=1,ncol=2, dimnames=list(c("Prop"), c("Q","H")))
aprop95[,c("Q")]<-Allele95[,c("Q")]/Allele95[,c("Total")]
aprop95[,c("H")]<-Allele95[,c("H")]/Allele95[,c("Total")]
Cod96<-matrix(0, nrow=1, ncol=4, dimnames=list(c("Count"), c("G/G", "G/S", "S/S", "Total")))
Cod96[,c("G/G")]<-sum(CodTab[,c("cod96")]==c("G/G"))
Cod96[,c("G/S")]<-sum(CodTab[,c("cod96")]==c("G/S"))
Cod96[,c("S/S")]<-sum(CodTab[,c("cod96")]==c("S/S"))
Cod96[,c("Total")]<-sum(Cod96)
prop96<-matrix(0, nrow=1, ncol=3, dimnames=list(c("Prop"), c("G/G", "G/S", "S/S")))
prop96[,c("G/G")]<-Cod96[,c("G/G")]/Cod96[,c("Total")]
prop96[,c("G/S")]<-Cod96[,c("G/S")]/Cod96[,c("Total")]
prop96[,c("S/S")]<-Cod96[,c("S/S")]/Cod96[,c("Total")]
Allele96<-matrix(0, nrow=1, ncol=3, dimnames=list(c("Count"), c("G", "S","Total")))
Allele96[,c("G")]<-(2*sum(CodTab[,c("cod96")]==c("G/G")))+sum(CodTab[,c("cod96")]==c("G/S"))
Allele96[,c("S")]<-(2*sum(CodTab[,c("cod96")]==c("S/S")))+sum(CodTab[,c("cod96")]==c("G/S"))
Allele96[,c("Total")]<-sum(Allele96)
aprop96<-matrix(0,nrow=1,ncol=2, dimnames=list(c("Prop"), c("G","S")))
aprop96[,c("G")]<-Allele96[,c("G")]/Allele96[,c("Total")]
aprop96[,c("S")]<-Allele96[,c("S")]/Allele96[,c("Total")]
Cod116<-matrix(0, nrow=1, ncol=4, dimnames=list(c("Count"), c("A/A", "A/G", "G/G", "Total")))
Cod116[,c("A/A")]<-sum(CodTab[,c("cod116")]==c("A/A"))
Cod116[,c("A/G")]<-sum(CodTab[,c("cod116")]==c("A/G"))
Cod116[,c("G/G")]<-sum(CodTab[,c("cod116")]==c("G/G"))
Cod116[,c("Total")]<-sum(Cod116)
prop116<-matrix(0, nrow=1, ncol=3, dimnames=list(c("Prop"), c("A/A", "A/G", "G/G")))
prop116[,c("A/A")]<-Cod116[,c("A/A")]/Cod116[,c("Total")]
prop116[,c("A/G")]<-Cod116[,c("A/G")]/Cod116[,c("Total")]
prop116[,c("G/G")]<-Cod116[,c("G/G")]/Cod116[,c("Total")]
Allele116<-matrix(0, nrow=1, ncol=3, dimnames=list(c("Count"), c("A", "G","Total")))
Allele116[,c("A")]<-(2*sum(CodTab[,c("cod116")]==c("A/A")))+sum(CodTab[,c("cod116")]==c("G/G"))
Allele116[,c("G")]<-(2*sum(CodTab[,c("cod116")]==c("G/G")))+sum(CodTab[,c("cod116")]==c("A/G"))
Allele116[,c("Total")]<-sum(Allele116)
aprop116<-matrix(0,nrow=1,ncol=2, dimnames=list(c("Prop"), c("A","G")))
aprop116[,c("A")]<-Allele116[,c("A")]/Allele116[,c("Total")]
aprop116[,c("G")]<-Allele116[,c("G")]/Allele116[,c("Total")]
GenProp<-matrix(0, nrow=3,ncol=3, dimnames=list(c("Homozygote Major", "Heterozygote", "Homozygote Minor"), c("cod95","cod96","cod116")))
GenProp[,c("cod95")]<-t(prop95)
GenProp[,c("cod96")]<-t(prop96)
GenProp[,c("cod116")]<-t(prop116)
AlleleProp<-matrix(0, nrow=2, ncol=3, dimnames=list(c("Major", "Minor"), c("cod95", "cod96", "cod116")))
AlleleProp[,c("cod95")]<-t(aprop95)
AlleleProp[,c("cod96")]<-t(aprop96)
AlleleProp[,c("cod116")]<-t(aprop116)
GenProp<-list(GenProp, AlleleProp, prop95, prop96, prop116, aprop95, aprop96, aprop116)
names(GenProp)<-c("Genotype","Allele", "Geno95", "Geno96", "Geno116", "Allele95", "Allele96", "Allele116")
return(GenProp)
}
if(x=="ODHE"){
CodTab<-as.matrix(CodTab[!rownames(CodTab)%in% c("Ref"),])
colnames(CodTab)<-c("cod225")
Cod225<-matrix(0, nrow=1, ncol=4, dimnames=list(c("Count"), c("S/S", "S/F", "F/F", "Total")))
Cod225[,c("S/S")]<-sum(CodTab[,c("cod225")]==c("S/S"))
Cod225[,c("S/F")]<-sum(CodTab[,c("cod225")]==c("S/F"))
Cod225[,c("F/F")]<-sum(CodTab[,c("cod225")]==c("F/F"))
Cod225[,c("Total")]<-sum(Cod225)
prop225<-matrix(0, nrow=1, ncol=3, dimnames=list(c("Prop"), c("S/S", "S/F", "F/F")))
prop225[,c("S/S")]<-Cod225[,c("S/S")]/Cod225[,c("Total")]
prop225[,c("S/F")]<-Cod225[,c("S/F")]/Cod225[,c("Total")]
prop225[,c("F/F")]<-Cod225[,c("F/F")]/Cod225[,c("Total")]
Allele225<-matrix(0, nrow=1, ncol=3, dimnames=list(c("Count"), c("S", "F", "Total")))
Allele225[,c("S")]<-(2*sum(CodTab[,c("cod225")]==c("S/S")))+sum(CodTab[,c("cod225")]==c("S/F"))
Allele225[,c("F")]<-(2*sum(CodTab[,c("cod225")]==c("F/F")))+sum(CodTab[,c("cod225")]==c("F/F"))
aprop225<-matrix(0,nrow=1,ncol=2, dimnames=list(c("Prop"), c("S","F")))
aprop225[,c("S")]<-Allele225[,c("S")]/Allele225[,c("Total")]
aprop225[,c("F")]<-Allele225[,c("F")]/Allele225[,c("Total")]
GenProp<-matrix(0, nrow=3,ncol=1, dimnames=list(c("Homozygote Major", "Heterozygote", "Homozygote Minor"), c("cod225")))
GenProp[,c("cod225")]<-t(prop225)
AlleleProp<-matrix(0, nrow=2, ncol=1, dimnames=list(c("Major", "Minor"), c("cod225")))
AlleleProp[,c("cod225")]<-t(aprop225)
GenProp<-list(GenProp, AlleleProp, prop225, aprop225)
names(GenProp)<-c("Genotype","Allele", "Geno225", "Allele225")
return(GenProp)
}
if(x=="other"){
CodTab<-CodTab
col<-colnames(CodTab)
CodTab<-as.matrix(CodTab[!rownames(CodTab)%in% c("Ref"),])
colnames(CodTab)<-col
colnames(CodTab)<-paste("cod", colnames(CodTab), sep="")
codname<-colnames(CodTab)
CodTab[CodTab=="Error"]<-NA
er<-as.matrix(CodTab[rowSums(is.na(CodTab))>0,])
er<-rownames(er)
CodTab<-CodTab[!rownames(CodTab)%in% er,]
CodTab<-as.matrix(CodTab)
labels<-list()
for(i in 1:ncol(CodTab)){
labels[[i]]<-unique(na.omit(CodTab[,i]))
labels[[i]]<-strsplit(labels[[i]], split="/")
labels[[i]]<-as.vector(unlist(labels[[i]]))
labels[[i]]<-unique(na.omit(labels[[i]]))
labels[[i]]<-sort(labels[[i]])
}
names(labels)<-codname
n1<-vector()
for(i in 1:length(labels)){
n1[[i]]<-length(labels[[i]])
}
if(n1<2){
labels1<-subset(labels, n1<2)
for(i in 1:length(labels1)){
labels1[[i]]<-c(paste(labels1[[i]][1], labels1[[i]][1], sep="/"), paste(labels1[[i]][1], c("-"), sep="/"), paste(c("-"),c("-"), sep="/"))
}
labels2<-labels1
}
if(n1==2){
labels2<-subset(labels, n1==2)
for(i in 1:length(labels2)){
labels2[[i]]<-c(paste(labels2[[i]][1], labels2[[i]][1], sep="/"), paste(labels2[[i]][1], labels2[[i]][2], sep="/"), paste(labels2[[i]][2], labels2[[i]][2], sep="/"))
}
labels2<-labels2
}
if(n1==2&n1<2){
labels1<-subset(labels, n1<2)
for(i in 1:length(labels1)){
labels1[[i]]<-c(paste(labels1[[i]][1], labels1[[i]][1], sep="/"), paste(labels1[[i]][1], c("-"), sep="/"), paste(c("-"),c("-"), sep="/"))
}
labels2<-subset(labels, n1==2)
for(i in 1:length(labels2)){
labels2[[i]]<-c(paste(labels2[[i]][1], labels2[[i]][1], sep="/"), paste(labels2[[i]][1], labels2[[i]][2], sep="/"), paste(labels2[[i]][2], labels2[[i]][2], sep="/"))
}
labels2<-append(labels1,labels2)
}
GenSum<-list()
for(i in 1:length(labels2)){
GenSum[[i]]<-matrix(0, nrow=1,ncol=4)
rownames(GenSum[[i]])<-c("Count")
colnames(GenSum[[i]])<-c(labels2[[i]][1],labels2[[i]][2],labels2[[i]][3], "Total")
}
names(GenSum)<-names(labels2)
CodTab<-as.matrix(CodTab)
for(i in 1:length(GenSum)){
GenSum[[i]][1,1]<-sum(CodTab[,i]==labels2[[i]][1])
GenSum[[i]][1,2]<-sum(CodTab[,i]==labels2[[i]][2])
GenSum[[i]][1,3]<-sum(CodTab[,i]==labels2[[i]][3])
GenSum[[i]][1,4]<-sum(GenSum[[i]][1,1:3])
}
GenProp<-matrix(0,3,length(GenSum), dimnames=list(c("Homozygote A", "Heterozygote", "Homozygote B"), names(GenSum)))
for(i in 1:length(GenSum)){
GenProp[1,i]<-(GenSum[[i]][1,1]/GenSum[[i]][1,4])
GenProp[2,i]<-(GenSum[[i]][1,2]/GenSum[[i]][1,4])
GenProp[3,i]<-(GenSum[[i]][1,3]/GenSum[[i]][1,4])
}
AlleleProp<-matrix(0, 2, ncol(GenProp), dimnames=list(c("Allele A", "Allele B"),colnames(GenProp)))
for(i in 1:length(GenSum)){
AlleleProp[1,i]<-((2*GenSum[[i]][1,1])+(GenSum[[i]][1,2]))/(2*GenSum[[i]][1,4])
AlleleProp[2,i]<-((2*GenSum[[i]][1,3])+(GenSum[[i]][1,2]))/(2*GenSum[[i]][1,4])
}
labels3<-list()
for(i in 1:length(labels2)){
labels3[[i]]<-labels2[[i]][2]
labels3[[i]]<-strsplit(labels3[[i]], split="/")
}
GProp<-list()
for(i in 1:length(GenSum)){
GProp[[i]]<-t(GenProp[,i])
colnames(GProp[[i]])<-unlist(labels2[[i]])
rownames(GProp[[i]])<-c("Prop")
}
AProp<-list()
for(i in 1:length(GenSum)){
AProp[[i]]<-t(AlleleProp[,i])
colnames(AProp[[i]])<-unlist(labels3[[i]])
rownames(AProp[[i]])<-c("Prop")
}
GenoLab<-paste("Geno", col, sep="")
AlleleLab<-paste("Allele", col, sep="")
GenProp<-c(list(GenProp), list(AlleleProp), GProp, AProp)
names(GenProp)<-c("Genotype", "Allele", GenoLab, AlleleLab)
return(GenProp)
}
}
if(Pop==T){
if(x=="CECA"){
CodTab<-as.matrix(CodTab[!rownames(CodTab)%in% c("Ref"),])
colnames(CodTab)<-c("cod132")
CodTab<-cbind(PopLabels, CodTab)
PopLabels<-unique(CodTab[,1])
PopList<-list()
for(i in 1:length(unique(CodTab[,1]))){
PopList[[i]]<-CodTab[CodTab[,1]==PopLabels[i],]
}
Cod132<-list()
for(i in 1:length(PopList)){
Cod132[[i]]<-matrix(0, nrow=1, ncol=4, dimnames=list(c("Count"), c("M/M", "M/L", "L/L", "Total")))
Cod132[[i]][,c("M/M")]<-sum(PopList[[i]][,c("cod132")]==c("M/M"))
Cod132[[i]][,c("M/L")]<-sum(PopList[[i]][,c("cod132")]==c("M/L"))
Cod132[[i]][,c("L/L")]<-sum(PopList[[i]][,c("cod132")]==c("L/L"))
Cod132[[i]][,c("Total")]<-sum(Cod132[[i]])
}
prop132<-list()
for(i in 1:length(PopList)){
prop132[[i]]<-matrix(0, nrow=1, ncol=3, dimnames=list(c("Prop"), c("M/M", "M/L", "L/L")))
prop132[[i]][,c("M/M")]<-Cod132[[i]][,c("M/M")]/Cod132[[i]][,c("Total")]
prop132[[i]][,c("M/L")]<-Cod132[[i]][,c("M/L")]/Cod132[[i]][,c("Total")]
prop132[[i]][,c("L/L")]<-Cod132[[i]][,c("L/L")]/Cod132[[i]][,c("Total")]
}
Allele132<-list()
for(i in 1:length(PopList)){
Allele132[[i]]<-matrix(0, nrow=1, ncol=3, dimnames=list(c("Count"), c("M", "L", "Total")))
Allele132[[i]][,c("M")]<-(2*sum(PopList[[i]][,c("cod132")]==c("M/M")))+sum(PopList[[i]][,c("cod132")]==c("M/L"))
Allele132[[i]][,c("L")]<-(2*sum(PopList[[i]][,c("cod132")]==c("L/L")))+sum(PopList[[i]][,c("cod132")]==c("M/L"))
Allele132[[i]][,c("Total")]<-sum(Allele132[[i]])
}
aprop132<-list()
for(i in 1:length(Allele132)){
aprop132[[i]]<-matrix(0,nrow=1,ncol=2, dimnames=list(c("Prop"), c("M","L")))
aprop132[[i]][,c("M")]<-Allele132[[i]][,c("M")]/Allele132[[i]][,c("Total")]
aprop132[[i]][,c("L")]<-Allele132[[i]][,c("L")]/Allele132[[i]][,c("Total")]
}
GenProp<-list()
for(i in 1:length(prop132)){
GenProp[[i]]<-matrix(0, nrow=3,ncol=1, dimnames=list(c("Homozygote Major", "Heterozygote", "Homozygote Minor"), c("cod132")))
GenProp[[i]][,c("cod132")]<-t(prop132[[i]])
}
AlleleProp<-list()
for(i in 1:length(aprop132)){
AlleleProp[[i]]<-matrix(0, nrow=2, ncol=1, dimnames=list(c("Major", "Minor"), c("cod132")))
AlleleProp[[i]][,c("cod132")]<-t(aprop132[[i]])
}
GenAll<-list()
for(i in 1:ncol(GenProp[[1]])){
GenAll[[i]]<-matrix(0,length(GenProp),3, dimnames=list(c(PopLabels),c("Homozygote Major", "Heterozygote", "Homozygote Minor")))
}
for(i in 1:length(GenProp)){