qtl (version 1.66)

pull.geno: Pull out the genotype data from a cross

Description

Pull out the genotype data from a cross object, as a single big matrix.

Usage

pull.geno(cross, chr)

Value

A matrix of size n.ind x tot.mar. The raw genotype data in the input cross object, with the chromosomes pasted together.

Arguments

cross

An object of class cross. See read.cross for details.

chr

Optional vector indicating the chromosomes to consider. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding - to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.

Author

Karl W Broman,

See Also

pull.pheno, pull.map pull.draws, pull.genoprob, pull.argmaxgeno

Examples

data(listeria)
dat <- pull.geno(listeria)

# image of the genotype data
image(1:ncol(dat),1:nrow(dat),t(dat),ylab="Individuals",xlab="Markers",
      col=c("red","yellow","blue","green","violet"))
abline(v=cumsum(c(0,nmar(listeria)))+0.5)
abline(h=nrow(dat)+0.5)