add.individuals {synbreed} | R Documentation |
This function extends an object of class gpData
by adding new
phenotypes, genotypes and pedigree.
add.individuals( gpData, pheno = NULL, geno = NULL, pedigree = NULL, covar = NULL, repl = NULL )
gpData |
object of class |
pheno |
|
geno |
|
pedigree |
|
covar |
|
repl |
The column of the pheno |
colnames
in geno
, pheno
and pedigree
must match
existing names in gpData
object.
object of class gpData
with new individuals
Valentin Wimmer
add.markers
, discard.individuals
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) # new phenotypic data newPheno <- data.frame(Yield = 200, Height = 100, row.names = "newLine") # simulating genotypic data newGeno <- matrix(sample(c("A", "A/B", "B"), ncol(gp$geno), replace = TRUE), nrow = 1) rownames(newGeno) <- "newLine" # new pedigree newPedigree <- create.pedigree(ID = "newLine", Par1 = 0, Par2 = 0, gener = 0) gp2 <- add.individuals(gp, pheno = newPheno, geno = newGeno, pedigree = newPedigree) ## Not run: # add one new DH line to maize data library(synbreedData) data(maize) newDHpheno <- data.frame(Trait = 1000, row.names = "newDH") # simulating genotypic data newDHgeno <- matrix(sample(c(0, 1), ncol(maize$geno), replace = TRUE), nrow = 1) rownames(newDHgeno) <- "newDH" # new pedigree newDHpedigree <- create.pedigree(ID = "newDH", Par1 = 0, Par2 = 0, gener = 0) # new covar information newDHcovar <- data.frame(family = NA, DH = 1, tbv = 1000, row.names = "newDH") # add individual maize2 <- add.individuals(maize, newDHpheno, newDHgeno, newDHpedigree, newDHcovar) summary(maize2) ## End(Not run)