genphen: 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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Genetic association studies have become an essential tool for studying the relationship between genotypes and phenotypes. They are necessary for the discovery of disease-causing genetic variants. Here we provide a tool for conducting genetic association studies, which uses statistical learning techniques such as random forests and support vector machines, as well as using Bayesian inference with Bayesian hierarchical models. These techniques are superior to the commonly used (frequentist) statistical approaches, alleviating the multiple hypothesis problems and the need for P value corrections, which often lead to massive numbers of false negatives. Thus, with genphen we provide a framework to compare the results obtained using frequentist methods with those obtained using the more sophisticated methods provided by this tool. The tool also provides a few visualization functions which enable the user to inspect the results of such genetic association study and conveniently select the genotypes which have the highest strength of association with the phenotype.

Author
Simo Kitanovski
Date of publication
None
Maintainer
Simo Kitanovski <simo.kitanovski@uni-due.de>
License
GPL (>= 2)
Version
1.2.0

View on Bioconductor

Man pages

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...
plotManhattan
Visualizing genphen results with Manhattan plots
plotSpecificGenotype
Visualizing specific genotypes
runGenphenBayes
Conducting genetic association analysis with Bayesian...
runGenphenRf
Conducting genetic association analysis with random forest
runGenphenSvm
Conducting genetic association analysis with linear support...

Files in this package

genphen/DESCRIPTION
genphen/NAMESPACE
genphen/R
genphen/R/genphen.R
genphen/R/plot.R
genphen/R/utility.R
genphen/build
genphen/build/vignette.rds
genphen/data
genphen/data/genotype.saap.RData
genphen/data/genotype.saap.msa.RData
genphen/data/genotype.snp.RData
genphen/data/genotype.snp.msa.RData
genphen/data/phenotype.saap.RData
genphen/data/phenotype.snp.RData
genphen/inst
genphen/inst/CITATION
genphen/inst/NEWS.Rd
genphen/inst/doc
genphen/inst/doc/genphenManual.R
genphen/inst/doc/genphenManual.Rnw
genphen/inst/doc/genphenManual.pdf
genphen/inst/extdata
genphen/inst/extdata/genotype.saap.fasta
genphen/inst/extdata/genotype.snp.fasta
genphen/inst/extdata/ndist.txt
genphen/inst/extdata/tdist.txt
genphen/man
genphen/man/genotype.saap.Rd
genphen/man/genotype.saap.msa.Rd
genphen/man/genotype.snp.Rd
genphen/man/genotype.snp.msa.Rd
genphen/man/phenotype.saap.Rd
genphen/man/phenotype.snp.Rd
genphen/man/plotGenphenBayes.Rd
genphen/man/plotGenphenRfSvm.Rd
genphen/man/plotManhattan.Rd
genphen/man/plotSpecificGenotype.Rd
genphen/man/runGenphenBayes.Rd
genphen/man/runGenphenRf.Rd
genphen/man/runGenphenSvm.Rd
genphen/vignettes
genphen/vignettes/fig1.pdf
genphen/vignettes/fig2.pdf
genphen/vignettes/fig3.pdf
genphen/vignettes/fig4.pdf
genphen/vignettes/genphenManual.Rnw