solarius: An R Interface to SOLAR

SOLAR is the standard software program to perform linkage and association mappings of the quantitative trait loci (QTLs) in pedigrees of arbitrary size and complexity. This package allows the user to exploit the variance component methods implemented in SOLAR. It automates such routine operations as formatting pedigree and phenotype data. It also parses the model output and contains summary and plotting functions for exploration of the results. In addition, solarius enables parallel computing of the linkage and association analyses, that makes the calculation of genome-wide scans more efficient. See <http://solar.txbiomedgenetics.org/> for more information about SOLAR.

AuthorAndrey Ziyatdinov [cre, aut], Helena Brunel [aut], Angel Martinez-Perez [aut], Alfonso Buil [aut], Alexandre Perera [cph], Jose Manuel Soria [cph]
Date of publication2015-12-13 16:51:09
MaintainerAndrey Ziyatdinov <andrey.ziyatdinov@upc.edu>
LicenseGPL (>= 3)
Version0.3.0.2
https://github.com/ugcd/solarius

View on CRAN

Man pages

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

dat50: dat50 data set adapted from FFBSKAT 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: Get a parameter value from 'solarius' models.

package.file: Alternative to system.file

plotKinship2: Plot the double kinship matrix

plotPed: Plot the pedigree

plotQQManh: Plot the association results

plotRes: Plot the residuals of a polygenic model

readPhen: Read plain-text table files phen and ped

snp2solar: 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.

solarPolyAssoc: S3 class solarPolyAssoc.

solarPolygenic: Run polygenic analysis.

solarPolygenicClass: 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.

Functions

annotate Man page
annotateSNPs Man page
availableTransforms Man page
dat30 Man page
df2solar Man page
explainedVarProp Man page
genocovdat30 Man page
genocovdata Man page
genodata Man page
getFormulaStr Man page
histKinship2 Man page
imageKinship2 Man page
kin Man page
loadExamplesPhen Man page
loadMulticPhen Man page
mapdat30 Man page
matchIdNames Man page
matchMapNames Man page
modelPar Man page
modelParCores Man page
modelParCPUtime Man page
modelParNumBatches Man page
package.file Man page
phenodata Man page
plotKinship2 Man page
plotManh Man page
plotPed Man page
plotQQ Man page
plotRes Man page
plotResQQ Man page
plot.solarAssoc Man page
plot.solarMultipoint Man page
print.solarAssoc Man page
print.solarBaeysAvgPolygenic Man page
print.solarMultipoint Man page
print.solarMultivar Man page
print.solarPolyAssoc Man page
print.solarPolygenic Man page
readPhen Man page
residuals.solarPolygenic Man page
snpcovdata2solar Man page
snpdata Man page
snpdata2solar Man page
snpmap2solar Man page
solar Man page
solarAssoc Man page
solarAssocClass Man page
solarBaeysAvgPolygenicClass Man page
solarKinship2 Man page
solarMultipoint Man page
solarMultipointClass Man page
solarMultivarClass Man page
solarPar Man page
solarParCovlistChi Man page
solarParCovlistP Man page
solarParH2rP Man page
solarParIndividuals Man page
solarParKurtosis Man page
solarParPvar Man page
solarParRhoP Man page
solarParRhoPOK Man page
solarParRhoPP Man page
solarParRhoPSE Man page
solarPolyAssoc Man page
solarPolygenic Man page
solarPolygenicClass Man page
solarReadFiles Man page
summary.solarAssoc Man page
summary.solarBaeysAvgPolygenic Man page
summary.solarMultipoint Man page
summary.solarPolygenic Man page
tabplot Man page
tabplot.solarMultipoint Man page
transformData Man page
transformTrait Man page

Files

solarius
solarius/TODO
solarius/inst
solarius/inst/examples
solarius/inst/examples/plot-regression.R
solarius/inst/examples/example-fields.R
solarius/inst/examples/example-h2r-height-GenABEL.R
solarius/inst/examples/function-solarMultivar.R
solarius/inst/examples/solar-multipoint-gait1.R
solarius/inst/examples/package-multic.R
solarius/inst/examples/extdata-solarOutput.R
solarius/inst/examples/function-solarAssoc.R
solarius/inst/examples/function-solarBayesAvg.R
solarius/inst/examples/solar-multipoint.R
solarius/inst/examples/solar-load.R
solarius/inst/examples/solar-mibd-incomplete.R
solarius/inst/examples/example-pedfile-snpStats.R
solarius/inst/examples/example-asssoc-snpStats.R
solarius/inst/tests
solarius/inst/tests/test-snpmap.R
solarius/inst/tests/test-solarPar.R
solarius/inst/tests/test-mgafiles.R
solarius/inst/tests/test-solarMultipoint.R
solarius/inst/tests/test-genocov.R
solarius/inst/tests/test-kinship.R
solarius/inst/tests/test-not-passed.R
solarius/inst/tests/test-plinkfiles.R
solarius/inst/tests/test-solarAssoc-parallel.R
solarius/inst/tests/test-solarAssoc.R
solarius/inst/tests/test-household.R
solarius/inst/tests/test-snplist.R
solarius/inst/tests/test-annotate.R
solarius/inst/extdata
solarius/inst/extdata/solarOutput
solarius/inst/extdata/solarOutput/simulated.ped
solarius/inst/extdata/solarOutput/phi2.gz
solarius/inst/extdata/solarOutput/solarMibdsCsvIncomplete
solarius/inst/extdata/solarOutput/solarMibdsCsvIncomplete/mibd.5.0.gz
solarius/inst/extdata/solarOutput/solarMibdsCsvIncomplete/mibd.5.1.gz
solarius/inst/extdata/solarOutput/solarMibds
solarius/inst/extdata/solarOutput/solarMibds/mibd.5.3.gz
solarius/inst/extdata/solarOutput/solarMibds/mibd.5.0.gz
solarius/inst/extdata/solarOutput/solarMibds/mibd.2.1.gz
solarius/inst/extdata/solarOutput/solarMibds/mibd.2.5.gz
solarius/inst/extdata/solarOutput/solarMibds/mibd.5.5.gz
solarius/inst/extdata/solarOutput/solarMibds/mibd.5.1.gz
solarius/inst/extdata/solarOutput/solarMibds/mibd.2.0.gz
solarius/inst/extdata/solarOutput/solarMibds/mibd.2.3.gz
solarius/inst/extdata/solarOutput/solarMibds/mibd.5.2.gz
solarius/inst/extdata/solarOutput/solarMibds/mibd.5.4.gz
solarius/inst/extdata/solarOutput/solarMibds/mibd.2.2.gz
solarius/inst/extdata/solarOutput/solarMibds/mibd.2.4.gz
solarius/inst/extdata/solarOutput/simulated.phen
solarius/inst/extdata/solarOutput/pedindex.cde
solarius/inst/extdata/solarOutput/pedindex.out
solarius/inst/extdata/solarOutput/solarMibdsCsv
solarius/inst/extdata/solarOutput/solarMibdsCsv/mibd.5.3.gz
solarius/inst/extdata/solarOutput/solarMibdsCsv/mibd.5.0.gz
solarius/inst/extdata/solarOutput/solarMibdsCsv/mibd.2.1.gz
solarius/inst/extdata/solarOutput/solarMibdsCsv/mibd.2.5.gz
solarius/inst/extdata/solarOutput/solarMibdsCsv/mibd.5.5.gz
solarius/inst/extdata/solarOutput/solarMibdsCsv/mibd.5.1.gz
solarius/inst/extdata/solarOutput/solarMibdsCsv/mibd.2.0.gz
solarius/inst/extdata/solarOutput/solarMibdsCsv/mibd.2.3.gz
solarius/inst/extdata/solarOutput/solarMibdsCsv/mibd.5.2.gz
solarius/inst/extdata/solarOutput/solarMibdsCsv/mibd.5.4.gz
solarius/inst/extdata/solarOutput/solarMibdsCsv/mibd.2.2.gz
solarius/inst/extdata/solarOutput/solarMibdsCsv/mibd.2.4.gz
solarius/inst/extdata/solarAssoc
solarius/inst/extdata/solarAssoc/ncdf
solarius/inst/extdata/solarAssoc/ncdf/dat50.scan
solarius/inst/extdata/solarAssoc/ncdf/dat50.snp
solarius/inst/extdata/solarAssoc/ncdf/dat50.ncdf
solarius/inst/extdata/solarAssoc/snp.genocov4
solarius/inst/extdata/solarAssoc/snp.geno-list1
solarius/inst/extdata/solarAssoc/dat.snp
solarius/inst/extdata/solarAssoc/map.snp.1.2
solarius/inst/extdata/solarAssoc/snp.genocov2
solarius/inst/extdata/solarAssoc/snp.geno-list
solarius/inst/extdata/solarAssoc/snp.genocov
solarius/inst/extdata/solarAssoc/dat.snp3
solarius/inst/extdata/solarAssoc/snp.genocov1
solarius/inst/extdata/solarAssoc/plink
solarius/inst/extdata/solarAssoc/plink/dat50.tfam
solarius/inst/extdata/solarAssoc/plink/dat50.map
solarius/inst/extdata/solarAssoc/plink/dat50.tped
solarius/inst/extdata/solarAssoc/plink/dat50.raw
solarius/inst/extdata/solarAssoc/plink/dat50.ped
solarius/inst/extdata/solarAssoc/dat.snp2
solarius/inst/extdata/solarAssoc/snp.genocov3
solarius/inst/extdata/solarAssoc/dat.snp1
solarius/inst/extdata/solarAssoc/map.snp.1.3
solarius/inst/extdata/solarAssoc/dat.snp4
solarius/inst/extdata/solarAssoc/map.snp.1.4
solarius/inst/extdata/solarAssoc/snp.geno-list2
solarius/inst/extdata/solarAssoc/snp.geno-list4
solarius/inst/extdata/solarAssoc/map.snp.1.1
solarius/inst/extdata/solarAssoc/snp.geno-list3
solarius/inst/extdata/solarAssoc/map.snp.1
solarius/NAMESPACE
solarius/NEWS
solarius/data
solarius/data/dat50.RData
solarius/data/dat30.RData
solarius/data/datalist
solarius/R
solarius/R/transforms.lib.R solarius/R/solarMultivar.R solarius/R/solarBayesAvg.R solarius/R/classSolarPolygenic.R solarius/R/solarMultipoint.R solarius/R/classSolarAssoc.R solarius/R/files.lib.R solarius/R/plot.lib.R solarius/R/solarAssoc.R solarius/R/solarPolygenic.R solarius/R/solarPolyAssoc.R solarius/R/solarPar.R solarius/R/support.lib.R solarius/R/solar.lib.R solarius/R/package.R solarius/R/polygenic.lib.R solarius/R/classSolarMultipoint.R solarius/R/multipoint.lib.R solarius/R/assoc.lib.R solarius/R/modelPar.R solarius/R/datasets.R solarius/R/data.lib.R
solarius/README.md
solarius/MD5
solarius/DESCRIPTION
solarius/man
solarius/man/df2solar.Rd solarius/man/readPhen.Rd solarius/man/explainedVarProp.Rd solarius/man/annotate.Rd solarius/man/solarPolygenicClass.Rd solarius/man/solarBaeysAvgPolygenicClass.Rd solarius/man/solarPolygenic.Rd solarius/man/solarReadFiles.Rd solarius/man/solarMultivarClass.Rd solarius/man/dat30.Rd solarius/man/solarAssocClass.Rd solarius/man/tabplot.Rd solarius/man/availableTransforms.Rd solarius/man/plotRes.Rd solarius/man/transformTrait.Rd solarius/man/snp2solar.Rd solarius/man/solar.Rd solarius/man/dat50.Rd solarius/man/getFormulaStr.Rd solarius/man/solarAssoc.Rd solarius/man/matchIdNames.Rd solarius/man/loadExamplesPhen.Rd solarius/man/solarMultipoint.Rd solarius/man/modelPar.Rd solarius/man/solarKinship2.Rd solarius/man/annotateSNPs.Rd solarius/man/solarMultipointClass.Rd solarius/man/package.file.Rd solarius/man/plotKinship2.Rd solarius/man/solarPar.Rd solarius/man/solarPolyAssoc.Rd solarius/man/plotPed.Rd solarius/man/transformData.Rd solarius/man/loadMulticPhen.Rd solarius/man/matchMapNames.Rd solarius/man/plotQQManh.Rd

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