R: Plot permutation results for a 2d, 2-QTL genome scan

plot.scantwoperm {qtl} | R Documentation

## Plot permutation results for a 2d, 2-QTL genome scan

### Description

Plot a histogram of the permutation results from a two-dimensional, two-QTL genome scan.

### Usage

    ## S3 method for class 'scantwoperm'
    plot(x, lodcolumn=1, include_rug=TRUE, ...)

### Arguments

`x` | An object of class `"scantwoperm"`, as output by `scantwo` when `n.perm` is specified.
`lodcolumn` | This indicates the LOD score column to plot. This should be a single number between 1 and the number of LOD columns in the object input.
`include_rug` | If TRUE, include a call to `rug`.
`...` | Passed to the function `hist` when it is called.

### Details

The function plots a histogram of the permutation results obtained by `scantwo` when `n.perm` is specified. Separate histograms are provided for the five LOD scores, `full`, `fv1`, `int`, `add`, and `av1`.

### Value

None.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`scantwo`, `summary.scantwoperm`

### Examples

    data(fake.bc)
    fake.bc <- calc.genoprob(fake.bc)

    operm2 <- scantwo(fake.bc, method="hk", n.perm=10)
    plot(operm2)

[Package qtl version 1.46-2 Index]