discard.markers {synbreed} | R Documentation |
The function produces subsets from an object of class gpData
with reduced markers. Marker informartion will be discarded from elements geno
and map
discard.markers(gpData, which=NULL, whichNot=NULL)
gpData |
object of class |
which |
character vector identifying names of markers which get discarded in |
whichNot |
character vector identifying names of markers which get kept in |
Object of class gpData
Valentin Wimmer and Hans-Juergen Auinger
create.gpData
, add.markers
, add.individuals
, discard.individuals
# 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) ## End(Not run)