R: Pull out the genotype probabilities from a cross

pull.genoprob {qtl} | R Documentation

## Pull out the genotype probabilities from a cross

### Description

Pull out the results of `calc.genoprob` from a cross as a matrix.

### Usage

    pull.genoprob(cross, chr, omit.first.prob=FALSE,
                  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.
`omit.first.prob` | If TRUE, omit the probabilities for the first genotype at each position (since they sum to 1).
`include.pos.info` | If TRUE, include columns with marker name, genotype, chromosome ID, and cM position. (If `include.pos.info=TRUE`, we take `rotate=TRUE`.)
`rotate` | If TRUE, return matrix with individuals as columns and positions/genotypes as rows. If FALSE, rows correspond to individuals.

### Value

A matrix containing genotype probabilities. Multiple chromosomes and the multiple genotypes at each position are pasted together.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`pull.geno`, `pull.argmaxgeno`, `pull.draws`, `calc.genoprob`

### Examples

    data(listeria)
    listeria <- calc.genoprob(listeria, step=1, stepwidth="max")
    pr <- pull.genoprob(listeria, chr=c(5,13), omit.first.prob=TRUE, include.pos.info=TRUE, rotate=TRUE)
    pr[1:5,1:10]

[Package qtl version 1.46-2 Index]