discard.individuals {synbreed} | R Documentation |
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
.
discard.individuals(gpData, which=NULL, keepPedigree = FALSE, whichNot=NULL)
gpData |
object of class |
which |
character vector identifying names of individuals get discarded from a |
keepPedigree |
|
whichNot |
character vector identifying names of individuals get kept in a |
Object of class gpData
Valentin Wimmer and Hans-Juergen Auinger
create.gpData
, add.individuals
, add.markers
, discard.markers
# 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)