Help topics

  • annotate
    Annotate SNPs in association study
  • annotateSNPs
    Annotate SNPs
  • availableTransforms
    Get a list of available transforms.
  • dat30(genocovdat30, mapdat30)
    dat30 data set adapted from multic R package
  • df2solar
    Export phenotype and pedigree data into SOLAR files
  • explainedVarProp
    Get explained variances for a group of SOLAR models.
  • getFormulaStr
    Get formula string from a solarPolygenic object
  • loadExamplesPhen
    Load the example data (GAW10) from SOLAR.
  • loadMulticPhen
    Load the complete data set from R package multic
  • matchIdNames
    Match ID column names
  • matchMapNames
    Match map column names
  • modelPar(modelParCPUtime, modelParCores, modelParNumBatches)
    Get a parameter value from
  • package.file
    Alternative to system.file
  • phenodata(genocovdata, genodata, kin, snpdata)
    dat50 data set adapted from FFBSKAT R package
  • plotKinship2(histKinship2, imageKinship2)
    Plot the double kinship matrix
  • plotManh(plotQQ)
    Plot the association results
  • plotPed
    Plot the pedigree
  • plotRes(plotResQQ)
    Plot the residuals of a polygenic model
  • readPhen
    Read plain-text table files phen and ped
  • snpdata2solar(snpcovdata2solar, snpmap2solar)
    Export snp genotypes, genotype covariates and amp to SOLAR
  • solar
    Call SOLAR program from R
  • solarAssoc
    Run association analysis.
  • solarAssocClass(plot.solarAssoc, print.solarAssoc, summary.solarAssoc)
    S3 class solarAssoc.
  • solarBaeysAvgPolygenicClass(print.solarBaeysAvgPolygenic, summary.solarBaeysAvgPolygenic)
    S3 class solarBaeysAvgPolygenic
  • solariusPackage(solariusPackage-package)
    solarius: an R package wrapper to SOLAR.
  • solarKinship2
    Compute empirical double kinship matrix by SOLAR
  • solarMultipoint
    Run multipoint linkage analysis.
  • solarMultipointClass(plot.solarMultipoint, print.solarMultipoint, summary.solarMultipoint, tabplot.solarMultipoint)
    S3 class solarMultipoint.
  • solarMultivarClass(print.solarMultivar)
    S3 class solarMultivar.
  • solarPar(solarParCovlistChi, solarParCovlistP, solarParH2rP, solarParIndividuals, solarParKurtosis, solarParPvar, solarParRhoP, solarParRhoPOK, solarParRhoPP, solarParRhoPSE)
    Get a parameter value from SOLAR model files.
  • solarPolyAssoc(print.solarPolyAssoc)
    S3 class solarPolyAssoc.
  • solarPolygenic
    Run polygenic analysis.
  • solarPolygenicClass(print.solarPolygenic, residuals.solarPolygenic, summary.solarPolygenic)
    S3 class solarPolygenic.
  • solarReadFiles
    Read SOLAR output files in a directory
  • tabplot
    S3 method tabplot
  • transformData
    Apply transforms to a data set.
  • transformTrait
    Transform a trait.


  • Imports: methods, plyr, ggplot2, data.table
  • Suggests: tools, kinship2, scales, Matrix, gdata, doParallel, iterators, parallel, qqman, rsnps, grid, gridExtra


  • Andrey Ziyatdinov [cre, aut]
  • Helena Brunel [aut]
  • Angel Martinez-Perez [aut]
  • Alfonso Buil [aut]
  • Alexandre Perera [cph]
  • Jose Manuel Soria [cph]