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.


Note: Manuscript of the package entitled as "solarius: an R interface to SOLAR for variance component analysis in pedigrees" is under revision in Bioinformatics journal.

R package wrapper to SOLAR

library(devtools)
install_github("ugcd/solarius")
  • do not automate things in R, which SOLAR has already automated
    • call SOLAR from system.call with options and settings parameters
  • make it more R self-content and independent on other programs
    • phenotypes format as data.frame
    • make use of R plots like plotting pedigrees
    • make use of parallelization insfrastructure available in R
    • do not rely on tcl scripts anymore
  • get rid of salamboR artifacts (ancestor of solarius)
    • GAIT-specific functions
    • interface with other programs than SOLAR
    • lost version-control traces
    • dependence on old-school code from previous mantainers
    • dependence on (many) tcl scripts
  • get rid of SOLAR artifacts
    • store models/phenos in folders/files
  • make use of github infrastructure: collaborative coding, issues, gh-pages, etc
  • Designed for the family-based studies (HHID, PROBND, FAMID)
    • support for extended pedigrees
  • Optimization routines for computing VC
  • Advanced polygenic models
    • support for multivariate models
    • liability threshold model
    • LRT applied to both covariates and variance components
  • Elaborated linkage models
    • Multi-pass
    • Multivariate
    • Adjustment of LOD scores
  • Association models
    • Speed-up with residuals
  • Advanced VC models
    • Sex-specificity (custom scripts)
    • Longitudinal (custom scripts)
  • Interactive environment for data manipulation
  • Graphics
    • Plot residuals, QQ-plot, Manhattan plot
  • Parallel computing
# load library
library(solarius)
 
# load data set for running polygenic and linkage models
data(dat30)
 
# univariate polygenic model
mod1 <- solarPolygenic(trait1 ~ age + sex, dat30, covtest = TRUE)
 
# bivariate polygenic model
mod2 <- solarPolygenic(trait1 + trait2 ~ 1, dat30,
  polygenic.options = '-testrhoe -testrhog')
 
# specify directory with IBD matrices and run linkage model
mibddir <- system.file('extdata', 'solarOutput',
  'solarMibdsCsv', package = 'solarius') 
link <- solarMultipoint(trait1 ~ 1, dat30,
  mibddir = mibddir, chr = 5)
 
# load data set and run association model in parallel
data(dat50)
assoc <- solarAssoc(trait ~ age + sex, phenodata,
  kinship = kin, snpdata = genodata, cores = 2)

News

solarius 0.3.0

  • Support for Windows OS is depreciated because of SOLAR issues with Windows. OS_type: unix line is added to DESCRIPTION file.

solarius 0.2.4

  • Changes in response to the Reviewers' comments (the manuscript submitted to Bioinformatics).
    • NCBI2R package is replaced by rsnps package.
  • Added two series of functions solarPar* and solarModel* to extract parameters of SOLAR and solarius models, respectively.
  • Added tabplot S3 method for solarAssoc class.
  • Initiated new SOLAR models: solarPolyAssoc, solarBayesAvg and solarMultivar. Still under development.

solarius 0.2.3

  • Changes for the official release on CRAN.
    • doMC package is preferred to doParallel package (suggestion from CRAN maintainers).
    • require command is replaced by requireNamespace command.

solarius 0.2.2

  • All three main analyses (polygenic, association and linkage) are implemented.
  • A number of vignettes are provided.
    • http://ugcd.github.io/solarius/vignettes/tutorial.html
    • http://ugcd.github.io/solarius/vignettes/minimal.html
    • http://ugcd.github.io/solarius/vignettes/modelsGAIT1.html
  • The first version for CRAN is prepared.
  • LazyLoad for data is disabled.

solarius 0.1.1

  • The house-hold effect is processed. Expected fields in a data set include HHID and hhid. See inst/tests/test-household.R.
  • Other fields supported by SOLAR are MZTWIN, PROBND. See matchIdNames for more details.

solarius 0.1.0

  • Initial version.

Reference manual

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install.packages("solarius")

0.3.0.2 by Andrey Ziyatdinov, a year ago


https://github.com/ugcd/solarius


Browse source code at https://github.com/cran/solarius


Authors: Andrey Ziyatdinov [cre, aut], Helena Brunel [aut], Angel Martinez-Perez [aut], Alfonso Buil [aut], Alexandre Perera [cph], Jose Manuel Soria [cph]


Documentation:   PDF Manual  


GPL (>= 3) license


Imports methods, plyr, ggplot2, data.table

Suggests tools, kinship2, scales, Matrix, gdata, doParallel, iterators, parallel, qqman, rsnps, grid, gridExtra


See at CRAN