Nothing
library(AGHmatrix)
Gmatrix
inds <- 10
markers <- 100
markersdata <- matrix(sample(x=0:4, size=inds*markers, replace=TRUE), nrow=inds, ncol=markers)
markersdata
G1 <-Gmatrix(markersdata,ploidy=4,method="VanRaden")
G2 <-Gmatrix(markersdata,ploidy=4,method="Endelman")
SNPmatrix<-markersdata
inds <- 3
markers <- 4
markersdata <- matrix(sample(x=0:4, size=inds*markers, replace=TRUE), nrow=inds, ncol=markers)
Frequency <- colSums(SNPmatrix)/(nrow(SNPmatrix)*ploidy)
Frequency <- cbind(Frequency,1-Frequency)
Frequency <- cbind(apply(SNPmatrix, 2, function(x) alelleFreq(x,0))
, apply(SNPmatrix, 2, function(x) alelleFreq(x, 2)))
Q1 <- matrix(rep(c(9,4,25,16),3),nrow=3,byrow=TRUE)/144*6
Q2 <- matrix(c(0,4,10,4,
9,0,0,12,
0,0,15,0),nrow=3,byrow=TRUE)*3/12
Q3 <- matrix(c(0,2,2,0,
6,0,0,6,
0,0,6,0),nrow=3,byrow=TRUE)*0.5
Q<-Q1-Q2+Q3
tcrossprod(Q)/drop((6*crossprod(c(3/12,2/12,5/12,4/12)^2,c(1-c(3/12,2/12,5/12,4/12))^2)))
M1 <- matrix(c(0,2,2,1,
3,0,0,3,
0,0,3,0),nrow=3,byrow=TRUE)
M2 <-matrix(c(4,2,2,3,
1,4,4,1,
4,4,1,4),nrow=3,byrow=TRUE)
Gmatrix(M1,ploidy=4)
Gmatrix(M2,ploidy=4)
## Including Data from Endelman 2018
MolPotato <- read.table("~/git/AGHmatrix/data/FileS2.csv",header=TRUE,sep=",")
ind <- MolPotato[[1]]
MolPotato <- as.matrix(MolPotato[,-1])
rownames(MolPotato) <- ind
snp.potato <- MolPotato
save(snp.potato,file="snp.potato.rdata")
library(AGHmatrix)
G1 <- Gmatrix(MolPotato,ploidy=4)
G2 <- Gmatrix(MolPotato,ploidy=4,method="Slater")
G3 <- Gmatrix(MolPotato,ploidy=4,method="Endelman")
PedPotato <- read.table("~/git/AGHmatrix/data/FileS3.csv",header=TRUE,sep=",")
PedPotato[,2] <- PedPotato[PedPotato[,2],1]
PedPotato[which(PedPotato[,3]==0),3] <- NA
PedPotato[which(PedPotato[,4]==0),4] <- NA
PedPotato[,3] <- PedPotato[PedPotato[,3],1]
PedPotato[,4] <- PedPotato[PedPotato[,4],1]
ped.potato <- PedPotato[,c(2,3,4)]
ped.potato$GID <- as.character(ped.potato$GID)
ped.potato$Mother <- as.character(ped.potato$Mother)
ped.potato$Father <- as.character(ped.potato$Father)
ped.potato[which(is.na(ped.potato[,3])),3] <- "0"
ped.potato[which(is.na(ped.potato[,2])),2] <- "0"
A1<-Amatrix(ped.potato)
names(ped.potato)[1]<-"Ind"
A1<-Amatrix(ped.potato)
save(ped.potato,file="ped.potato.rdata")
data("snp.potato")
?Gmatrix
Gmatrix.VanRaden <- Gmatrix(snp.potato, method="VanRaden", ploidy=4)
Gmatrix.Endelman <- Gmatrix(snp.potato, method="Endelman", ploidy=4)
Gmatrix.Slater <- Gmatrix(snp.potato, method="Slater", ploidy=4)
Gmatrix.Pseudodiploid <- Gmatrix(snp.potato, method="VanRaden", ploidy=4, pseudo.diploid=TRUE)
Amatrix.potato <- Amatrix(ped.potato, ploidy=4)
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