An R Interface to SOLAR

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Documentation for package ‘solarius’ version 0.3.0.2

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