Description Usage Arguments Value Author(s) See Also Examples
The function produces subsets from an object of class gpData
with reduced markers. Marker informartion will be discarded from elements geno
and map
1 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | # 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)
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