discard.individuals {synbreed} | R Documentation |
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
.
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
# 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)