R: Pull out the results of the Viterbi algorithm from a cross

pull.argmaxgeno {qtl} | R Documentation

## Pull out the results of the Viterbi algorithm from a cross

### Description

Pull out the results of `argmax.geno` from a cross as a matrix.

### Usage

    pull.argmaxgeno(cross, chr, include.pos.info=FALSE, rotate=FALSE)

### 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.
`include.pos.info` | If TRUE, include columns with marker name, chromosmoe ID, and cM position. (If `include.pos.info=TRUE`, we take `rotate=TRUE`.)
`rotate` | If TRUE, return matrix with individuals as columns and positions as rows. If FALSE, rows correspond to individuals.

### Value

A matrix containing numeric indicators of the inferred genotypes. Multiple chromosomes are pasted together.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`pull.geno`, `pull.genoprob`, `pull.draws`, `argmax.geno`

### Examples

    data(listeria)
    listeria <- argmax.geno(listeria, step=1, stepwidth="max")
    amg <- pull.argmaxgeno(listeria, chr=c(5,13), include.pos.info=TRUE, rotate=TRUE)
    amg[1:5,1:10]

[Package qtl version 1.41-6 Index]