qtl (version 1.21-2)

max.scanone: 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, df=FALSE, na.rm=TRUE, \dots)

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 chromos

lodcolumn

An integer, indicating which of the LOD score columns should be considered in pulling out the peak (these are indexed 1, 2, ...).

df

If TRUE, the degrees of freedom associated with the LOD scores are shown.

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.

See Also

scanone, plot.scanone, summary.scanone

Examples

data(listeria)
listeria <- subset(listeria,chr=c(5,13),ind=!is.na(listeria$pheno[,1]))
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)