Package to deal with pedigree data

Description

Package with functions to analyse and transform pedigree data. A pedigree is a data.frame where the first column contains an ID, and the second and third columns contain ID of first and second parent.

Author(s)

Albart Coster: <albart.coster@wur.nl>

See Also

trimPed orderPed countGen makeA makeAinv calcInbreeding add.Inds

Function to add missing individuals to a pedigree

Description

Function add.Inds() adds missing individuals to a pedigree and returns the complete pedigree as a data.frame with the same headers as the original pedigree. Remeber to check for errors beforehand with function errors.ped. Unknown parents should be coded as NA.

Usage

add.Inds(ped)

Arguments

Value

data.frame of three columns with identical header as input.

Author(s)

Albart Coster, Albart.Coster@wur.nl

See Also

orderPed

Examples

ID <- 3:5
DAM <- c(1,1,3)
SIRE <- c(2,2,4)
pedigree <- data.frame(ID,DAM,SIRE)
pedigree <- add.Inds(pedigree)

Function to calculate breeding values using an animal model

Description

Fit an animal model to data, use a given variance ratio (\alpha = \frac{\sigma^2_e}{\sigma^ 2_a}). Calculate inverse of the additive genetic relationship matrix using function makeInv() of this package.

Usage

blup(formula, ped, alpha,trim = FALSE)

Arguments

Value

Vector of solutions to the model, including random animal effects.

See Also

SamplePedigree, gblup, makeAinv,blup

Examples

example(gblup)
sol <- blup(P~1,ped = ped,alpha = 1/h2 - 1)

Function to calculate a relationship matrix from marker data (usually allele count data), G matrix.

Description

Function to calculate a relationship matrix from marker data. Option to return the inverse of matrix. Inverse calculated using Matrix package.

Usage

calcG(M, data = NULL,solve = FALSE)

Arguments

Value

Matrix of class dgeMatrix.

See Also

SamplePedigree, gblup, makeAinv,blup

Examples

example(gblup)
G <- calcG(M)
Ginv <- calcG(M,solve = TRUE)

Calculates inbreeding coefficients for individuals in a pedigree.

Description

Calculates inbreeding coefficients of individuals in a pedigree.

Usage

calcInbreeding(ped)

Arguments

Value

Logical.

Examples

id <- 1:6
dam <- c(0,0,1,1,4,4)
sire <- c(0,0,2,2,3,5)
ped <- data.frame(id,dam,sire)
(F <- calcInbreeding(ped))

Count generation number for each individual in a pedigree.

Description

Counts generation number for individuals in a pedigreee.

Usage

countGen(ped)

Arguments

Value

Numeric vector

Examples

id <- 1:5
dam <- c(0,0,1,1,4)
sire <- c(0,0,2,2,3)
ped <- data.frame(id,dam,sire)
(gens <- countGen(ped))

Function that counts the number of offspring (and following generations for each individual in a pedigree.

Description

Function to count the number of offspring for each individual in a pedigree. With loops, offspring of later generations will be counted several times.

Usage

countOff(ped)

Arguments

Value

Numeric vector with number of offspring for each individual in the pedigree.

Author(s)

Albart Coster

Examples

example(countGen)
countOff(ped)

Function to calculate breeding values using an animal model and a relationship matrix calculated from the markers (G matrix)

Description

Fit an animal model to data, use a given variance ratio (\alpha = \frac{\sigma^2_e}{\sigma^ 2_a}). Calculate genetic relationship matrix using the function calcG of this package.

Usage

gblup(formula, data, M, lambda)

Arguments

Value

Vector of solutions to the model, including random animal effects.

See Also

SamplePedigree, gblup, makeAinv,blup

Examples

## Example Code from SampleHaplotypes
hList <- HaploSim::SampleHaplotypes(nHaplotypes = 20,genDist =
1,nDec = 3,nLoc = 20) ## create objects
h <- HaploSim::SampleHaplotype(H0 = hList[[1]],H1 = hList[[2]],genDist =
1,nDec = 3)

## code from the Example SamplePedigree
ID <- 1:10
pID0 <- c(rep(0,5),1,1,3,3,5)
pID1 <- c(rep(0,4),2,2,2,4,4,6)
ped <- data.frame(ID,pID0,pID1)
phList <- HaploSim::SamplePedigree(orig = hList,ped = ped)

## own code
h2 <- 0.5
ped <- phList$ped
hList <- phList$hList
qtlList <- HaploSim::ListQTL(hList = hList,frqtl = 0.1,sigma2qtl = 1)
qtl <- tapply(unlist(qtlList),list(rep(names(qtlList),times = unlist(lapply(qtlList,length))),
                   unlist(lapply(qtlList,function(x)seq(1,length(x))))),mean,na.rm = TRUE)
qtl <- reshape::melt(qtl)
names(qtl) <- c("POS","TRAIT","a")
HH <- HaploSim::getAll(hList,translatePos = FALSE)
rownames(HH) <- sapply(hList,function(x)x@hID)
QQ <- HH[,match(qtl$POS,colnames(HH))]
g <- QQ
ped$G <- with(ped,g[match(hID0,rownames(g))]+g[match(hID1,rownames(g))])
sigmae <- sqrt(var(ped$G)/h2 - var(ped$G))
ped$P <- ped$G + rnorm(nrow(ped),0,sigmae)
M <- with(ped,HH[match(hID0,rownames(HH)),] + HH[match(hID1,rownames(HH)),]) 
rownames(M) <- ped$ID
sol <- gblup(P~1,data = ped[,c('ID','P')],M = M,lambda = 1/h2 - 1)

Makes the A matrix for a part of a pedigree

Description

Makes the A matrix for a part of a pedigree and stores it in a file called A.txt.

Usage

makeA(ped,which)

Arguments

Value

Logical.

Examples

id <- 1:6
dam <- c(0,0,1,1,4,4)
sire <- c(0,0,2,2,3,5)
ped <- data.frame(id,dam,sire)
makeA(ped,which = c(rep(FALSE,4),rep(TRUE,2)))
A <- read.table("A.txt")

if(file.exists("A.txt"))
file.remove("A.txt")

Makes inverted A matrix for a pedigree

Description

Makes inverted A matrix for a pedigree and stores it in a file called Ainv.txt.

Usage

makeAinv(ped)

Arguments

Value

Logical.

Examples

id <- 1:6
dam <- c(0,0,1,1,4,4)
sire <- c(0,0,2,2,3,5)
ped <- data.frame(id,dam,sire)
makeAinv(ped)
Ai <- read.table('Ainv.txt')
nInd <- nrow(ped)
Ainv <- matrix(0,nrow = nInd,ncol = nInd)
Ainv[as.matrix(Ai[,1:2])] <- Ai[,3]
dd <- diag(Ainv)
Ainv <- Ainv + t(Ainv)
diag(Ainv) <- dd

if(file.exists("Ainv.txt"))
file.remove("Ainv.txt")

Orders a pedigree

Description

Orders a pedigree so that offspring follow parents.

Usage

orderPed(ped)

Arguments

Value

numerical vector

Examples

id <- 1:6
dam <- c(0,0,1,1,4,4)
sire <- c(0,0,2,2,3,5)
pedigree <- data.frame(id,dam,sire)
(ord <- orderPed(pedigree))
pedigree <- pedigree[6:1,]
(ord <- orderPed(pedigree))
pedigree <- pedigree[order(ord),]
pwrong <- pedigree
pwrong[1,2] <- pwrong[6,1]

Function to trim a pedigree based on available data

Description

Trims a pedigree given a vector of data. Branches without data are trimmed off the pedigree.

Usage

trimPed(ped, data,ngenback = NULL)

Arguments

Value

Logical vector specifying if an individual should stay in the pedigree.

Examples

id <- 1:5
dam <- c(0,0,1,1,4)
sire <- c(0,0,2,2,3)
data <- c(FALSE,FALSE,TRUE,FALSE,FALSE)
ped <- data.frame(id,dam,sire)
yn <- trimPed(ped,data)
ped <- ped[yn,]