SNPassoc.R
In gaawr2: Genetic Association Analysis

run_SNPassoc <- function()
{
  options.default <- options()
  options(width=200,digits=2)
  data(asthma, package = "SNPassoc")
  str(asthma, list.len=8)
  knitr::kable(asthma[1:3,1:8],caption="First three records & two SNPs")
  snpCols <- colnames(asthma)[6+(1:2)]
  snps <- SNPassoc::setupSNP(data=asthma[snpCols], colSNPs=1:length(snpCols), sep="")
  head(snps)
  summary(snps, print=FALSE)
  lapply(snps, head)
  lapply(snps, summary)
  SNPassoc::tableHWE(snps)

  asthma.snps <- asthma %>%
                 dplyr::rename(cc=casecontrol) %>%
                 SNPassoc::setupSNP(colSNPs=(6+1):ncol(.), sep="")
# Model 1: Simple SNP association with BMI
  SNPassoc::association(bmi ~ rs4490198, data = asthma.snps)

# Model 2: SNP association with case-control status
  SNPassoc::association(cc ~ rs4490198, data = asthma.snps)

# Model 3: SNP association with covariates (country and smoke)
  SNPassoc::association(cc ~ rs4490198 + country + smoke, data = asthma.snps)

# Model 4: SNP association with stratification by gender
  SNPassoc::association(cc ~ rs4490198 + survival::strata(gender), data = asthma.snps)

# Model 5: SNP association with subset (only Spain)
  SNPassoc::association(cc ~ rs4490198, data = asthma.snps, subset = country == "Spain")

# Model 6: Interaction between SNP (dominant model) and smoking
  SNPassoc::association(cc ~ SNPassoc::dominant(rs4490198) * factor(smoke), data = asthma.snps)

# Model 7: Interaction between two SNPs (dominant model for rs4490198)
  SNPassoc::association(cc ~ rs4490198 * factor(rs11123242), data = asthma.snps, model.interaction = "dominant")

  assoc <- SNPassoc::WGassociation(cc, data=asthma.snps, mc.cores=5)
  assoc %>%
  as.data.frame() %>%
  dplyr::select(-comments) %>%
  knitr::kable(caption="SNP association")
  assoc.adj <- SNPassoc::WGassociation(cc ~ country + smoke, asthma.snps, mc.cores=5)
  assoc.adj %>%
  as.data.frame() %>%
  dplyr::select(-comments) %>%
  knitr::kable(caption="with adjustment for contountry & smoking")
  assoc.maxstat <- SNPassoc::maxstat(asthma.snps, cc)
  knitr::kable(t(assoc.maxstat[,]),caption="Max stat association statistics")
  options(options.default)
}