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.

Author
Andrey Ziyatdinov [cre, aut], Helena Brunel [aut], Angel Martinez-Perez [aut], Alfonso Buil [aut], Alexandre Perera [cph], Jose Manuel Soria [cph]
Date of publication
2015-12-13 16:51:09
Maintainer
Andrey Ziyatdinov <andrey.ziyatdinov@upc.edu>
License
GPL (>= 3)
Version
0.3.0.2
URLs

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