Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/add.individuals.r
This function extends an object of class gpData
by adding new
phenotypes, genotypes and pedigree.
1 2 3 4 5 6 7 8 |
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
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 31 32 33 34 35 36 37 38 39 40 41 42 43 | 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.