R: Maximum peak in genome scan

max.scanone {qtl} | R Documentation

## Maximum peak in genome scan

### Description

Print the row of the output from `scanone` that corresponds to the maximum LOD, genome-wide.

### Usage

    ## S3 method for class 'scanone'
    max(object, chr, lodcolumn=1, na.rm=TRUE, ...)

### Arguments

`object` | An object of the form output by the function `scanone`: a data.frame whose third column is the LOD score.
`chr` | Optional vector indicating the chromosomes to consider. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding `-` to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.
`lodcolumn` | An integer, indicating which of the LOD score columns should be considered in pulling out the peak (these are indexed 1, 2, ...).
`na.rm` | A logical indicating whether missing values should be removed.
`...` | Ignored.

### Value

An object of class `summary.scanone`, to be printed by `print.summary.scanone`. This is a data.frame with one row, corresponding to the maximum LOD peak either genome-wide or for the particular chromosome specified.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`scanone`, `plot.scanone`, `summary.scanone`

### Examples

    data(listeria)

    listeria <- calc.genoprob(listeria, step=2.5)
    out <- scanone(listeria, model="2part", upper=TRUE)
    # Maximum peak for LOD(p,mu)
    max(out)

    # Maximum peak for LOD(p,mu) on chr 5
    max(out,chr=5)

    # Maximum peak for LOD(p,mu) on chromosomes other than chr 13
    max(out,chr="-13")

    # Maximum peak for LOD(p)
    max(out, lodcolumn=2)

    # Maximum peak for LOD(mu)
    max(out, lodcolumn=3)

[Package qtl version 1.46-2 Index]