profileplot {dlmap}R Documentation

Plot Wald profiles of interval mapping scans

Description

Plots the Wald statistic profile for each chromosome with detected QTL on first interval mapping scan. Indicates marker locations, marker names, and detected QTL positions obtained from a dlmap fit.

Usage

profileplot(object, ...)

## S3 method for class 'dlmap':
profileplot(object, chr, marker.names=TRUE, QTLpos=TRUE, pch=20, ...)

Arguments

object object of class dlmap
chr character string naming the subset of chromosomes to plot; or, if numeric, a vector of chromosome indices
marker.names logical value. if TRUE then marker names are plotted along the top of the plot. Defaults to TRUE
QTLpos logical value. if TRUE then QTL positions are indicated with vertical lines. Defaults to TRUE
pch Character to be used for points in plotting; default is solid circle
... arguments passed to "plot" to set up the plot region. Arguments may also be passed to "text" for the manipulation of the marker names

Details

The function profileplot provides a neat visual display of the Wald profile for chromosomes with detected QTL. If no QTL are detected, nothing will be plotted. Otherwise, the Wald profile will be plotted by cM position of points on the interval mapping grid. Marker names will be displayed at the appropriate positions along the top of the plot. Vertical lines will mark the position of detected QTL.

Value

The Wald profile from the first iteration of interval mapping scans is plotted for all selected chromosomes, with marker names, marker locations, and QTL positions displayed.

Author(s)

Emma Huang and Andrew George; Julian Taylor

References

Huang, BE and George, AW. 2009. Look before you leap: A new approach to QTL mapping. TAG 119:899-911

Examples

## Not run: 
# load dataset
data(BSdat)

dl.in1 <- dlcross(format="rqtl", obj=BSdat, idname="ID", fixpos=1)
BSdl <- dlmap.asreml(object=dl.in1, phename="phenotype", filestem="BS")
BSdl <- dlmap.lme(object=dl.in1, phename="phenotype", filestem="BS")

profileplot(BSdl)
## End(Not run)

[Package dlmap version 1.06 Index]