Man pages for solarius
An R Interface to SOLAR

annotateAnnotate SNPs in association study
annotateSNPsAnnotate SNPs
availableTransformsGet a list of available transforms.
dat30dat30 data set adapted from multic R package
dat50dat50 data set adapted from FFBSKAT R package
df2solarExport phenotype and pedigree data into SOLAR files
explainedVarPropGet explained variances for a group of SOLAR models.
getFormulaStrGet formula string from a solarPolygenic object
loadExamplesPhenLoad the example data (GAW10) from SOLAR.
loadMulticPhenLoad the complete data set from R package multic
matchIdNamesMatch ID column names
matchMapNamesMatch map column names
modelParGet a parameter value from 'solarius' models.
package.fileAlternative to system.file
plotKinship2Plot the double kinship matrix
plotPedPlot the pedigree
plotQQManhPlot the association results
plotResPlot the residuals of a polygenic model
readPhenRead plain-text table files phen and ped
snp2solarExport snp genotypes, genotype covariates and amp to SOLAR
solarCall SOLAR program from R
solarAssocRun association analysis.
solarAssocClassS3 class solarAssoc.
solarBaeysAvgPolygenicClassS3 class solarBaeysAvgPolygenic
solarKinship2Compute empirical double kinship matrix by SOLAR
solarMultipointRun multipoint linkage analysis.
solarMultipointClassS3 class solarMultipoint.
solarMultivarClassS3 class solarMultivar.
solarParGet a parameter value from SOLAR model files.
solarPolyAssocS3 class solarPolyAssoc.
solarPolygenicRun polygenic analysis.
solarPolygenicClassS3 class solarPolygenic.
solarReadFilesRead SOLAR output files in a directory
tabplotS3 method tabplot
transformDataApply transforms to a data set.
transformTraitTransform a trait.
solarius documentation built on May 2, 2019, 2:43 a.m.