R: Reduce to a grid of pseudomarkers.

reduce2grid {qtl} | R Documentation

## Reduce to a grid of pseudomarkers.

### Description

For high-density marker data, rather than run `scanone` at both the markers and at a set of pseudomarkers, we reduce to just a set of evenly-spaced pseudomarkers

### Usage

    reduce2grid(cross)

### Arguments

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

### Details

Genotype probabilities (from `calc.genoprob`) and/or imputations (from `sim.geno`) are subset to a grid of pseudomarkers.

This is so that, in the case of high-density markers, we can do the genome scan calculations at a smaller set of points (on an evenly-spaced grid, but not at the markers) to save computation time.

You need to first have run `calc.genoprob` and/or `sim.geno`, and you must use `stepwidth="fixed"`.

When plotting results with `plot.scanone`, use `incl.markers=FALSE`, as the output of `scanone` won't include information about the marker locations and so will plot tick marks only at the first marker on each chromosome.

### Value

The input `cross` object with included genotype probabilities or imputations subset to an evenly-spaced grid.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`calc.genoprob`, `sim.geno`, `scanone`, `plot.scanone`

### Examples

    data(hyper)
    hyper <- calc.genoprob(hyper, step=2)
    hypersub <- reduce2grid(hyper)

    ## Not run: out <- scanone(hypersub)
    plot(out, incl.markers=FALSE)
    ## End(Not run)

[Package qtl version 1.46-2 Index]