R: Create matrix of marker covariates for QTL analysis

formMarkerCovar {qtl} | R Documentation

## Create matrix of marker covariates for QTL analysis

### Description

Pull out a matrix of genotypes or genotype probabilities to use markers as covariates in QTL analysis.

### Usage

    formMarkerCovar(cross, markers, method=c("prob", "imp", "argmax"), ...)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`markers` | A vector of character strings of marker or pseudomarker names. Pseudomarker names may be of the form `"5@21.5"` (for chr 5 at 21.5 cM), but then all names must be of this form.
`method` | If `method="prob"`, the genotype probabilities from `calc.genoprob` are used; otherwise we use `fill.geno` to impute missing data, with this method.
`...` | Passed to `fill.geno`, if necessary.

### Value

A matrix containing genotype probabilities or genotype indicators, suitable for use as covariates in `scanone`.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`pull.geno`, `pull.genoprob`, `fill.geno`, `scanone`

### Examples

    data(hyper)
    hyper <- calc.genoprob(hyper, step=0)
    peakMarker <- "D4Mit164"
    X <- formMarkerCovar(hyper, peakMarker)

    out <- scanone(hyper, addcovar=X)

[Package qtl version 1.41-6 Index]