A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models

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Documentation for package ‘genphen’ version 1.6.0

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genotype.saap SAAP genotype dataset
genotype.saap.msa SAAP genotype dataset (msa)
genotype.snp SNP genotype dataset
genotype.snp.msa SNP genotype dataset (msa)
phenotype.saap Phenotype dataset
phenotype.snp Phenotype dataset
plotGenphenBayes Visualizing the genphen results of runGenphenBayes
plotGenphenRfSvm Visualizing the genphen results of runGenphenRf or runGenphenSvm
plotManhattan Visualizing genphen results with Manhattan plots
plotSpecificGenotype Visualizing specific genotypes
runGenphenBayes Conducting genetic association analysis with Bayesian inference, using hierarchical models.
runGenphenRf Conducting genetic association analysis with random forest
runGenphenSvm Conducting genetic association analysis with linear support vector machines (LSVM)