solarius

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

• Package on CRAN
• Documentation http://ugcd.github.io/solarius/doc/
• Vignettes
  • R code vignettes/
  • hmlt output:
    1. tutorial.html
    2. minimal.html
    3. modelsGAIT1.html
• Project web http://ugcd.github.io/solarius/ (under construction)

Install package

library(devtools)
install_github("ugcd/solarius")

References

• Appendix 1. SOLAR Command Descriptions
• SOLAR web page at txbiomedgenetics.org
• SOLAR Eclipse is a new collaboration to develop genetic analysis tools for imaging applications

Motivation

• 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

On the SOLAR side

• 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)

On the R side

• Interactive environment for data manipulation
• Graphics
  • Plot residuals, QQ-plot, Manhattan plot
• Parallel computing

Quick start

# 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)