mqmplotheatmap: Heatmap of a genome of MQM scan on multiple phenotypes

In qtl: Tools for Analyzing QTL Experiments

Heatmap of a genome of MQM scan on multiple phenotypes

Description

Plotting routine to display a heatmap of results obtained from a multiple-QTL model on multiple phenotypes (the output of mqmscanall)

Usage

mqmplot.heatmap(cross, result, directed=TRUE, legend=FALSE, breaks =
c(-100,-10,-3,0,3,10,100), col =
c("darkblue","blue","lightblue","yellow","orange","red"), ...)

Arguments

cross	An object of class cross. See read.cross for details.
result	Result object from mqmscanall, the object needs to be of class mqmmulti
directed	Take direction of QTLs into account (takes more time because of QTL direction calculations
legend	If TRUE, add a legend to the plot
breaks	Color break points for the LOD scores
col	Colors used between breaks
...	Additional arguments passed to the image function

Author(s)

Danny Arends [e-mail]

See Also

• The MQM tutorial: https://rqtl.org/tutorials/MQM-tour.pdf

• MQM - MQM description and references

• mqmscan - Main MQM single trait analysis

• mqmscanall - Parallellized traits analysis

• mqmaugment - Augmentation routine for estimating missing data

• mqmautocofactors - Set cofactors using marker density

• mqmsetcofactors - Set cofactors at fixed locations

• mqmpermutation - Estimate significance levels

• scanone - Single QTL scanning

Examples

data(multitrait)

multitrait <- fill.geno(multitrait) # impute missing genotype data
result <- mqmscanall(multitrait, logtransform=TRUE)
mqmplot.heatmap(multitrait,result)

qtl documentation built on Sept. 11, 2024, 5:43 p.m.