synbreed (version 0.12-6)

discard.markers:

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

# 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)
## ---------------------------------------------

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