Learn R Programming

MultiPhen

:exclamation: This is forked from the CRAN R package repository. MultiPhen — A Package to Test for Pleiotropic Effects

To run it you need to clone the repository and then run following in R (where path_to_file is the cloned directory) The following was tested in R-3.6.1

path_to_file = "C:/Users/LCOIN/github/MultiPhen"
INSTALL = TRUE
if(INSTALL){
install.packages("abind")
install.packages("epitools")
install.packages("meta")
install.packages("HardyWeinberg")
install.packages("RColorBrewer")
install.packages("gplots")
install.packages(path_to_file, repos = NULL, type="source")
}

Copy Link

Version

Install

install.packages('MultiPhen')

Monthly Downloads

284

Version

2.0.3

License

GPL-2

Maintainer

Last Published

February 9th, 2020

Functions in MultiPhen (2.0.3)

MultiPhen-internal

Internal MultiPhen objects
mPhen.options

Retrieves default mPhen options, and descriptions.
mPhen

A function for the genetic association testing of multiple phenotypes
mPhen.defineOptions

Defines and modifies options.
mPhen.plotCorrelation

Plots correlation between phenotype values conditional on genotype
mPhen.cca

Sparse canonical correlation analysis
mPhen.assoc

A function for the genetic association testing of multiple phenotypes
MultiPhen-package

MultiPhen, a package for the genetic association testing of multiple phenotypes
mPhen.preparePheno

Prepare phenotype data for analysis
mPhen.readGenotypes

Open, and read from a read connection to a genotype file
mPhen.writeOutput

Prepares output files and plots from MultiPhen results
read.plink

A function to read (small) binary PLINK binary files in a R session
snps.imputed

Imputed SNP dataset
mPhen.sampleCovar

Generates a covariance matrix.
mPhen.readPhenoFiles

Read and merge phenotype files
mPhen.simulate

Simulates phenotypes according to a correlation structure.
pheno

A dummy phenotype dataset that provides an example of the input phenotype data used by the package
mPhen.sampleGeno

Sample genotypes
snps

A dummy snp dataset that provides an example of the input snp data used by the package