discard.individuals: Subsets for objects of class gpData

In synbreed: Framework for the Analysis of Genomic Prediction Data using R

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

Author(s)

Valentin Wimmer and Hans-Juergen Auinger

See Also

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

Examples

# 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)


## End(Not run)

synbreed documentation built on May 2, 2019, 3:23 a.m.