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.

Files in this package

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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