R: Maximum peak in two-dimensional genome scan

max.scantwo {qtl} | R Documentation

## Maximum peak in two-dimensional genome scan

### Description

Print the pair of loci with the largest LOD score in the results of `scantwo`.

### Usage

    ## S3 method for class 'scantwo'
    max(object, lodcolumn=1,
        what=c("best", "full", "add", "int"),
        na.rm=TRUE, ...)

### Arguments

`object` | An object of class `scantwo`, the output of the function `scantwo`.
`lodcolumn` | If the scantwo results contain LOD scores for multiple phenotypes, this argument indicates which to use.
`what` | Indicates for which LOD score the maximum should be reported.
`na.rm` | Ignored.
`...` | Ignored.

### Details

This is very similar to the `summary.scantwo` function, though this pulls out one pair of positions.

If `what="best"`, we find the pair of positions at which the LOD score for the full model (2 QTL + interaction) is maximized, and then also print the positions on that same pair of chromosomes at which the additive LOD score is maximized.

In the other cases, we pull out the pair of positions with the largest LOD score; which LOD score is considered is indicated by the `what` argument.

### Value

An object of class `summary.scantwo`, to be printed by `print.summary.scantwo`, with the pair of positions with the maximum LOD score. (Which LOD score is considered is indicated by the `what` argument.)

### Output of addpair

Note that, for output from `addpair` in which the new loci are indicated explicitly in the formula, the summary provided by `max.scantwo` is somewhat special.

All arguments (except, of course, the input `object`) are ignored.

If the formula is symmetric in the two new QTL, the output has just two LOD score columns: `lod.2v0` comparing the full model to the model with neither of the new QTL, and `lod.2v1` comparing the full model to the model with just one new QTL.

If the formula is not symmetric in the two new QTL, the output has three LOD score columns: `lod.2v0` comparing the full model to the model with neither of the new QTL, `lod.2v1b` comparing the full model to the model in which the first of the new QTL is omitted, and `lod.2v1a` comparing the full model to the model with the second of the new QTL omitted.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`scantwo`, `plot.scantwo`, `summary.scantwo`

### Examples

    data(fake.f2)

    fake.f2 <- calc.genoprob(fake.f2, step=10)
    out.2dim <- scantwo(fake.f2, method="hk")
    max(out.2dim)

[Package qtl version 1.41-6 Index]