An R Interface to SOLAR

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Documentation for package ‘solarius’ version 0.2.3

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solariusPackage-package solarius: an R package wrapper to SOLAR.
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
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
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.solarMultipoint S3 class solarMultipoint.
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.
solariusPackage solarius: an R package wrapper to SOLAR.
solarKinship2 Compute empirical double kinship matrix by SOLAR
solarMultipoint Run multipoint linkage analysis.
solarMultipointClass S3 class solarMultipoint.
solarPolygenic Run polygenic analysis.
solarPolygenicClass S3 class solarPolygenic.
solarReadFiles Read SOLAR output files in a directory
summary.solarAssoc S3 class solarAssoc.
summary.solarMultipoint S3 class solarMultipoint.
summary.solarPolygenic S3 class solarPolygenic.
transformData Apply transforms to a data set.
transformTrait Transform a trait.