MultiPhen: A Package to Test for Pleiotropic Effects

Share:

Performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model).

Author
Lachlan Coin, Paul O'Reilly, Yotsawat Pompyen, Clive Hoggart and Federico Calboli
Date of publication
2015-07-06 19:18:09
Maintainer
Federico Calboli <federico.calboli@helsinki.fi>
License
GPL-2
Version
2.0.1

View on CRAN

Man pages

mPhen
A function for the genetic association testing of multiple...
mPhen.assoc
A function for the genetic association testing of multiple...
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...
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-internal
Internal MultiPhen objects
MultiPhen-package
MultiPhen, a package for the genetic association testing of...
pheno
A dummy phenotype dataset that provides an example of the...
read.plink
A function to read (small) binary PLINK binary files in a R...
snps
A dummy snp dataset that provides an example of the input snp...
snps.imputed
Imputed SNP dataset

Files in this package

MultiPhen
MultiPhen/inst
MultiPhen/inst/doc
MultiPhen/inst/doc/MultiPhen.R
MultiPhen/inst/doc/MultiPhen.Rnw
MultiPhen/inst/doc/MultiPhen.pdf
MultiPhen/NAMESPACE
MultiPhen/demo
MultiPhen/demo/MultiPhen-demo.R
MultiPhen/demo/00Index
MultiPhen/data
MultiPhen/data/snps.imputed.rda
MultiPhen/data/snps.rda
MultiPhen/data/pheno.rda
MultiPhen/R
MultiPhen/R/mPhenSimulate.R
MultiPhen/R/MultiPhen-internal.R
MultiPhen/R/mPhenIO.R
MultiPhen/R/mPhen.R
MultiPhen/R/zzz.R
MultiPhen/vignettes
MultiPhen/vignettes/hapmap2.fam
MultiPhen/vignettes/ALL.chr21.integrated_phase1_v3.20101123.snps_indels_svs.genotypes_extract.impute
MultiPhen/vignettes/hapmap2.bim
MultiPhen/vignettes/ALL.chr21.integrated_phase1_v3.20101123.snps_indels_svs.genotypes_extract.vcf.gz
MultiPhen/vignettes/hapmap2.bed
MultiPhen/vignettes/ALL.chr21.integrated.phase1.v3.20101123.snps.indels.svs.genotypes.extract.impute
MultiPhen/vignettes/MultiPhen.Rnw
MultiPhen/vignettes/ALL.chr21.integrated.phase1.v3.20101123.snps.indels.svs.genotypes.extract.vcf.gz
MultiPhen/vignettes/pheno.txt
MultiPhen/vignettes/ALL.chr21.integrated_phase1_v3.20101123.snps_indels_svs.genotypes_extract.zip
MultiPhen/vignettes/ALL.chr21.integrated.phase1.v3.20101123.snps.indels.svs.genotypes.extract.zip
MultiPhen/MD5
MultiPhen/build
MultiPhen/build/vignette.rds
MultiPhen/DESCRIPTION
MultiPhen/man
MultiPhen/man/mPhen.cca.Rd
MultiPhen/man/pheno.Rd
MultiPhen/man/MultiPhen-internal.Rd
MultiPhen/man/mPhen.simulate.Rd
MultiPhen/man/snps.imputed.Rd
MultiPhen/man/mPhen.options.Rd
MultiPhen/man/mPhen.sampleGeno.Rd
MultiPhen/man/mPhen.plotCorrelation.Rd
MultiPhen/man/mPhen.sampleCovar.Rd
MultiPhen/man/mPhen.assoc.Rd
MultiPhen/man/mPhen.readGenotypes.Rd
MultiPhen/man/snps.Rd
MultiPhen/man/mPhen.writeOutput.Rd
MultiPhen/man/mPhen.preparePheno.Rd
MultiPhen/man/mPhen.defineOptions.Rd
MultiPhen/man/mPhen.readPhenoFiles.Rd
MultiPhen/man/mPhen.Rd
MultiPhen/man/MultiPhen-package.Rd
MultiPhen/man/read.plink.Rd