R: Add significance threshold to plot

add.threshold {qtl} | R Documentation

## Add significance threshold to plot

### Description

Add a significance threshold to a plot created by `plot.scanone`), using the permutation results.

### Usage

    add.threshold(out, chr, perms, alpha=0.05, lodcolumn=1, gap=25, ...)

### Arguments

`out` | An object of class `"scanone"`, as output by `scanone`. This must be identical to what was used in the call to `plot.scanone`.
`chr` | Optional vector specifying which chromosomes to plot. If a selected subset of chromosomes were plotted, they must be specified here.
`perms` | Permutation results from `scanone`, used to calculate the significance threshold.
`alpha` | Significance level of the threshold.
`lodcolumn` | An integer indicating which of column in the permutation results should be used.
`gap` | Gap separating chromosomes (in cM). This must be identical to what was used in the call to `plot.scanone`.
`...` | Passed to the function `abline` when it is called.

### Details

This function allows you to add a horizontal line at the significance threshold to genome scan results plotted by `plot.scanone`.

The arguments `out`, `chr`, and `gap` must match what was used in the call to `plot.scanone`.

The argument `perms` must be specified. If X-chromosome-specific permutations were performed (via the argument `perm.Xsp` in the call to `scanone`), separate thresholds will be plotted for the autosomes and the X chromosome. These are calculated via the `summary.scanoneperm` function.

### Value

None.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`scanone`, `plot.scanone`, `summary.scanoneperm`, `xaxisloc.scanone`

### Examples

    data(hyper)
    hyper <- calc.genoprob(hyper)
    out <- scanone(hyper, method="hk")
    operm <- scanone(hyper, method="hk", n.perm=100, perm.Xsp=TRUE)

    plot(out, chr=c(1,4,6,15,"X"))
    add.threshold(out, chr=c(1,4,6,15,"X"), perms=operm, alpha=0.05)
    add.threshold(out, chr=c(1,4,6,15,"X"), perms=operm, alpha=0.1,
                  col="green", lty=2)

[Package qtl version 1.41-6 Index]