qtl (version 0.92-3)

summary.scanone: Summarize the results of a genome scan

Description

Print the rows of the output from scanone that correspond to the maximum LOD for each chromosome, provided that they exceed a specified threshold.

Usage

summary.scanone(object, threshold=0, ...)

Arguments

object

An object of the form output by the function scanone: a data.frame whose first column is the chromosome ID and third column is the LOD score. All other columns are ignored.

threshold

Only peaks with LOD score above this value will be returned.

...

Ignored at this point.

Value

• An object of class summary.scanone, to be printed by print.summary.scanone. This is a data.frame with one row per chromosome, corresponding to the maximum LOD scores.

See Also

scanone, plot.scanone

Examples

data(listeria)
listeria <- calc.genoprob(listeria, step=2.5)
out <- scanone(listeria, model="2part")
# All peaks
summary(out)

# Peaks for LOD(p,mu)
summary(out, 5)

# peaks for LOD(p)
summary(out[,-3],3)

# peaks for LOD(mu)
summary(out[,-(3:4)],3)