R: Pull out the genotype data from a cross

pull.geno {qtl} | R Documentation

## 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)

### 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.

### Value

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

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### 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)

[Package qtl version 1.41-6 Index]