Directory

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.