This procedure visualizes the results obtained using the functions runGenphenRf or runGenphenSvm.
data.frame resulting from runGenphenRf/runGenphenSvm.
This procedure plots the results of the functions runGenphenRf or runGenphenSvm. Each association is shown as a point with respect to its effect size (Cohen's d) and the classification accuracy (CA). The colors of the points correspond to the Cohen's kappas. The confidence intervals estimated for the CA point estimates are provided here as well.
ggplot plot object.
Simo Kitanovski <firstname.lastname@example.org>
runGenphenRf, runGenphenSvm, plotGenphenBayes, plotSpecificGenotype, plotManhattan
1 2 3 4 5 6 7 8 9 10 11
#Example 1 (RF results): data(genotype.snp) #or data(genotype.snp.msa) in this case you cannot subset genotype.snp[, 1:5] data(phenotype.snp) genphen.rf <- runGenphenRf(genotype = genotype.snp[, 1:5], phenotype = phenotype.snp, cv.fold = 0.66, cv.steps = 100, hdi.level = 0.99, ntree = 1000) plotGenphenRfSvm(genphen.results = genphen.rf)