gelowin / solarius

R package to interface SOLAR

solarius

R package wrapper to SOLAR

• Vignettes SOALR models
  • R code vignettes/
  • hmlt output:
    1. modelsGAIT1.html
    2. models.html

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

Ideas

• 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

Current status

TODO

Polygenic model:

• extract residuals and make plots for them

Association model:

• think of which formats to support except the SOLAR one

Linkage model:

• make use of all linkage options availabe in SOLAR: second-path, adjustment of inflated scores

Content of Software Manual

TODO:

• Polygenic model (univariate)
  • house-hold effect
  • screen covariates
  • SOLAR options (polygenic.settings, polygenic.options)
• Polygenic model (bivariate)
  • Trouble-shooting
• Association model
  • parallelization (options(cores = 2))
• Linkage model

Examples

See tutorial page.

Data sets

Examples given here make use of dat30 data set distributed with solarius package. These are simulated data, and this data set was originally created in multic package and stored there in files. The version dat30 of the data set is a subset for famid < 30, and it is stired in *.RData file.

dat30 data set is lazy loaded. Hence, the user just needs to load the package:

library(solarius)