Description Usage Arguments Value Author(s) See Also Examples
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
.
1 | 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
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 30 | # 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)
|
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