discard.markers: Subsets for objects of class gpData

In synbreed: Framework for the Analysis of Genomic Prediction Data using R

Description

The function produces subsets from an object of class gpData with reduced markers. Marker informartion will be discarded from elements geno and map

Usage

discard.markers(gpData, which = NULL, whichNot = NULL)

Arguments

gpData	object of class gpData
which	character vector identifying names of markers which get discarded in geno from a gpData-object.
whichNot	character vector identifying names of markers which get kept in geno from a gpData-object. Overwrites argument which!

Value

Object of class gpData

Author(s)

Valentin Wimmer and Hans-Juergen Auinger

See Also

create.gpData, add.markers, add.individuals, discard.individuals

Examples

# 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)

synbreed documentation built on March 12, 2021, 3:01 a.m.