In ugcd/solarius: An R Interface to SOLAR

References

• http://helix.nih.gov/Documentation/solar-6.6.2-doc/09.chapter.html, Section 9.2.1.2 Multivariate Mu

Parameters

dir <- "solar"

Include

library(devtools)

Load

load_all("~/git/ugcd/solarius/")

Data

data(dat30, package = "solarius")

Polygenic

Model 1

mod1 <- solarPolygenic(trait1 + trait2 ~ age, dat30, dir = dir)

Model 2

cmd1 <- c("load model trait1.trait2/null0",
  "define age_i = age",
  "mu = mu + {t2*(<bage_i(trait2)>*age_i)}",
  "maximize",
  "save model trait1.trait2/custom1")

ret1 <- solar(cmd1, dir)

cmd2 <- c(
  "load model trait1.trait2/spor",
  "set loglik_0 [loglike]",
  "puts \"loglik_0 = $loglik_0\"",
  "load model trait1.trait2/null0",
  "set loglik_1 [loglike]",
  "puts \"loglik_1 = $loglik_1\"",
  "define age_i = age",
  "covariate sex age_i(trait2)",
  "polymod", 
  "maximize",
  "set loglik_2 [loglike]",
  "puts \"loglik_2 = $loglik_2\"",
  "save model trait1.trait2/custom2") 

ret2 <- solar(cmd2, dir)  

grep("loglik_", ret2, value = TRUE)

Association

Assoc 1

assoc1 <- solarAssoc(trait1 + trait2 ~ age, dat30, snpcovdata = genocovdat30[, 1:2], 
  dir = dir, 
  assoc.options = "-saveall")

SOLAR command:

assoc1$assoc$solar$cmd

ugcd/solarius documentation built on May 3, 2019, 2:22 p.m.