synbreed (version 0.12-9)

discard.markers: Subsets for objects of class gpData

Description

The function produces subsets from an object of class gpData with reduced markers. Marker informartion will be discarded from elements geno and map

Usage

discard.markers(gpData, which=NULL, whichNot=NULL)

Arguments

gpData

object of class gpData

which

character vector identifying names of markers which get discarded in geno from a gpData-object.

whichNot

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

Value

Object of class gpData

See Also

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

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)

# remove unmapped SNP M5 (which has no postion in the map)
gp2 <- discard.markers(gp,"M5")
summary(gp2)

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

# delete markers
maize2 <- discard.individuals(maize,colnames(maize$geno)[1:50])
summary(maize2)
# }