Package: MultiPhen 2.0.3

Lachlan Coin

MultiPhen: A Package to Test for Multi-Trait Association

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

Authors:Lachlan Coin, Paul O'Reilly, Yotsawat Pompyen, Clive Hoggart and Federico Calboli

MultiPhen_2.0.3.tar.gz
MultiPhen_2.0.3.tar.gz(r-4.5-noble)MultiPhen_2.0.3.tar.gz(r-4.4-noble)
MultiPhen_2.0.3.tgz(r-4.4-emscripten)MultiPhen_2.0.3.tgz(r-4.3-emscripten)
MultiPhen.pdf |MultiPhen.html✨
MultiPhen/json (API)

# Install 'MultiPhen' in R:

install.packages('MultiPhen', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

pheno - A dummy phenotype dataset that provides an example of the input phenotype data used by the package
snps - A dummy snp dataset that provides an example of the input snp data used by the package
snps.imputed - Imputed SNP dataset

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.93 score 17 scripts 299 downloads 29 mentions 199 exports 73 dependencies

Last updated 5 years agofrom:c365747889. Checks:OK: 1 NOTE: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 04 2024
R-4.5-linux	NOTE	Dec 04 2024

Exports:.abf .abfSig .allFreq .applySidakCorrection .applyTrans .as.numeric1 .backwardSelection .bafratio .calcExpectedGeno .calcOffset .calcPPA .centralise .chol .cholesky .closeGenoConnection .cnt .cntNa .cntVec .cnvdistr .convAvgToUnc .convAvgToUncM .convAvgToUncMat .convertFactorToMatrix .convertMatrixToFactor .countIn .destandardise .entropy .estSigma .expand .expand2 .expandCoeff .expandDat .expandGenoToDist .expandGenoToDistAll .expDist .extractIds .extractIdsMat .extractIdsVec .extractNames .extractSig .extractSig1 .extractSig1P .extractSigExact .extractSigP .fillMissing .findIn .findInclusion .findInd .findmax .fisherPvalue .fixDuplicatesInTodo .fixGenoCols .fixNonNumeric .flatten .flattenBetaX .formatTable .fprint .genRandCovar .getArray .getAvg .getAvgAll .getAvgWeights .getCNProfile .getDim .getFamily .getGlm .getHist .getHWE .getIMatrix .getin .getin1 .getin2 .getIncl .getLast .getLimitMatrixFromList .getMaf .getOnes .getPv .getPvLrr .getPvLrrAllGen .getPvLrrMult .getPvLrrMultiGen .getPvLrrMultiGen1 .getPvLrrMultiGenNoVS .getPvLrrMultiGenVS .getPvRev .getPvRevPleio .getPvRevPleio_.getPvRevPleioVS .getPvTable .getSuffix .getSumBetaX .getUNum1Matrix .getVCFDimNames .getVCFProcess .getVCFSplit .glm1 .gs .heatm .hwep .hwepall .hwestat .iscase .joinRes .joinResVec .length .lrt .mabf .mafCount .makeColsForBed .makeFactor .makeGenoWeights .makeNumeric .makeQuantile .makeThresh .makeTopTail .manh .manhattan .manhattanBed .mergeAlleleCols .mergeFiles .mergeLists .metaAnalysis .metaresFisher .metaresHetMeasure .metaresInvVarianceFixed .minOneMinus .mod .mod1 .mPhen .nonNumeric .nonNumeric1 .nullDim .numLev .nyholdtSidak .openGenoConnection .openOutputConnection .openPlinkConnection .openVCFConnection .openZipConnection .ordTest .ordTest1 .ordTest2 .ordTestUnivariate .orthogonalise .parseOpts .pFromSEBeta .plotBaf .plotFingerprint .pow .proc .proc1 .projOut .pseudoInv .qb .qq .qqplot .readGenoConnection .readHeader .readLimitFile .readLinesPlink .readPhen .readPlinkConnection .readVCFConnection .readZip .readZipConnection .reduceWeightsToGeno .reopenConnection .rescale .sampDirichlet .sampJoint .sample1 .seFromPBeta .splitImputed .standardise .subSample .sum1 .summariseBootstrap .tabulateWithWeights .trL .unchanged .updateRelatedness .updateSampleQC .writeBed .writeTable mPhen mPhen.assoc mPhen.cca mPhen.defineOptions mPhen.options mPhen.plotCorrelation mPhen.preparePheno mPhen.readGenotypes mPhen.readPhenoFiles mPhen.sampleCovar mPhen.sampleGeno mPhen.simulate mPhen.writeOutput read.plink

Dependencies:abind backports bit bit64 boot broom cli clipr codetools CompQuadForm cpp11 crayon dplyr epitools fansi forcats foreach generics glmnet glue HardyWeinberg haven hms iterators jomo lattice lifecycle lme4 magrittr MASS mathjaxr Matrix meta metadat metafor mice minqa mitml nlme nloptr nnet numDeriv ordinal pan pbapply pillar pkgconfig prettyunits progress purrr R6 RColorBrewer Rcpp RcppEigen readr rlang rpart Rsolnp shape stringi stringr survival tibble tidyr tidyselect truncnorm tzdb ucminf utf8 vctrs vroom withr xml2

Using MultiPhen for simulation

Rendered fromMultiPhen.Rnwusingutils::Sweaveon Dec 04 2024.

Last update: 2014-01-08
Started: 2014-01-08

Citation

Readme and manuals

Help Manual

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