genphen

Package: genphen
Type: Package
Title: A tool for computing genotype-phenotype associations using
statistical learning techniques
Version: 1.0.0
Date: 2016-03-20
Author: Simo Kitanovski
Maintainer: Simo Kitanovski <simo.kitanovski@uni-due.de>
Description: Given a set of genetic polymorphisms in the form of single
nucleotide poylmorphisms or single amino acid polymorphisms and
a corresponding phenotype data, often we are interested to
quantify their association such that we can identify the causal
polymorphisms. Using statistical learning techniques such as
random forests and support vector machines, this tool provides
the means to estimate genotype-phenotype associations. It also
provides visualization functions which enable the user to
visually inspect the results of such genetic association study
and conveniently select the genotypes which have the highest
strenght ofassociation with the phenotype.
License: GPL (>= 2)
Depends: R (>= 3.3), randomForest, e1071, ggplot2, effsize, Biostrings
LazyLoad: yes
biocViews: GenomeWideAssociation, Regression, Classification,
SupportVectorMachine, Genetics, SequenceMatching
NeedsCompilation: no
Packaged: 2016-05-04 06:51:58 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'genphen' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'genphen'
    finding HTML links ... done
    genotype.saap                           html  
    genotype.saap.msa                       html  
    genotype.snp                            html  
    genotype.snp.msa                        html  
    genphenSAAP                             html  
    genphenSNP                              html  
    phenotype.saap                          html  
    phenotype.snp                           html  
    plotGenphenResults                      html  
    plotManhattan                           html  
    plotSpecificGenotype                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genphen)
Making 'packages.html' ... done