A Package to Test for Multi-Trait Association

Documentation for package ‘MultiPhen’ version 2.0.3

MultiPhen-package	MultiPhen, a package for the genetic association testing of multiple phenotypes
mPhen	A function for the genetic association testing of multiple phenotypes
mPhen.assoc	A function for the genetic association testing of multiple phenotypes
mPhen.cca	Sparse canonical correlation analysis
mPhen.defineOptions	Defines and modifies options.
mPhen.options	Retrieves default mPhen options, and descriptions.
mPhen.plotCorrelation	Plots correlation between phenotype values conditional on genotype
mPhen.preparePheno	Prepare phenotype data for analysis
mPhen.readGenotypes	Open, and read from a read connection to a genotype file
mPhen.readPhenoFiles	Read and merge phenotype files
mPhen.sampleCovar	Generates a covariance matrix.
mPhen.sampleGeno	Sample genotypes
mPhen.simulate	Simulates phenotypes according to a correlation structure.
mPhen.writeOutput	Prepares output files and plots from MultiPhen results
MultiPhen	MultiPhen, a package for the genetic association testing of multiple phenotypes
pheno	A dummy phenotype dataset that provides an example of the input phenotype data used by the package
read.plink	A function to read (small) binary PLINK binary files in a R session
snps	A dummy snp dataset that provides an example of the input snp data used by the package
snps.imputed	Imputed SNP dataset