synbreed (version 0.12-9)

discard.individuals: Subsets for objects of class gpData

Description

The function produce subsets from an object of class gpData with reduced individuals. Individual information will be discarded from elements geno, pheno, covar and pedigree.

Usage

discard.individuals(gpData, which=NULL, keepPedigree = FALSE, whichNot=NULL)

Arguments

gpData

object of class gpData

which

character vector identifying names of individuals get discarded from a gpData-object.

keepPedigree

logical. Should the individual only be removed from elements geno and pheno but kept in the pedigree?

whichNot

character vector identifying names of individuals get kept in a gpData-object. Overwrites argument which!

Value

Object of class gpData

See Also

create.gpData, add.individuals, add.markers, discard.markers

Examples

# NOT RUN {
# example data
set.seed(311)
pheno <- data.frame(Yield = rnorm(10,200,5),Height=rnorm(10,100,1))
rownames(pheno) <- letters[1:10]
geno <- matrix(sample(c("A","A/B","B",NA),size=120,replace=TRUE,
prob=c(0.6,0.2,0.1,0.1)),nrow=10)
rownames(geno) <-  letters[1:10]
colnames(geno) <- paste("M",1:12,sep="")
# one SNP is not mapped (M5)
map <- data.frame(chr=rep(1:3,each=4),pos=rep(1:12))
map  <- map[-5,]
rownames(map) <- paste("M",c(1:4,6:12),sep="")
gp <- create.gpData(pheno=pheno,geno=geno,map=map)
summary(gp)

# discard genotypes with missing values in the marker matrix
gp3 <- discard.individuals(gp,names(which(rowSums(is.na(gp$geno))>0)))
summary(gp3)

# }
# NOT RUN {
# add one new DH line to maize data
library(synbreedData)
data(maize)

# delete individual
maize2 <- discard.individuals(maize,rownames(maize$geno)[1:10])
summary(maize2)

# }