qtl (version 1.66)

mqmplot.heatmap: 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

Danny Arends

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 <- subset(multitrait, chr=1:2, ind=!apply(multitrait$pheno, 1, function(a) any(is.na(a))))
multitrait$pheno <- multitrait$pheno[,1:3]
multitrait <- fill.geno(multitrait) # impute missing genotype data
result <- mqmscanall(multitrait, logtransform=TRUE)
mqmplot.heatmap(multitrait,result)