alpha: Genetic Components of Alcoholism

alphaR Documentation

Genetic Components of Alcoholism


Levels of expressed alpha synuclein mRNA in three groups of allele lengths of NACP-REP1.




A data frame with 97 observations on 2 variables.


allele length, a factor with levels "short", "intermediate" and "long".


expression levels of alpha synuclein mRNA.


Various studies have linked alcohol dependence phenotypes to chromosome 4. One candidate gene is NACP (non-amyloid component of plaques), coding for alpha synuclein. Bönsch et al. (2005) found longer alleles of NACP-REP1 in alcohol-dependent patients compared with healthy controls and reported that the allele lengths show some association with levels of expressed alpha synuclein mRNA.


Bönsch, D., Lederer, T., Reulbach, U., Hothorn, T., Kornhuber, J. and Bleich, S. (2005). Joint analysis of the NACP-REP1 marker within the alpha synuclein gene concludes association with alcohol dependence. Human Molecular Genetics 14(7), 967–971. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/hmg/ddi090")}


Hothorn, T., Hornik, K., van de Wiel, M. A. and Zeileis, A. (2006). A Lego system for conditional inference. The American Statistician 60(3), 257–263. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1198/000313006X118430")}

Winell, H. and Lindbäck, J. (2018). A general score-independent test for order-restricted inference. Statistics in Medicine 37(21), 3078–3090. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/sim.7690")}


## Boxplots
boxplot(elevel ~ alength, data = alpha)

## Asymptotic Kruskal-Wallis test
kruskal_test(elevel ~ alength, data = alpha)

## Asymptotic Kruskal-Wallis test using midpoint scores
kruskal_test(elevel ~ alength, data = alpha,
             scores = list(alength = c(2, 7, 11)))

## Asymptotic score-independent test
## Winell and Lindbaeck (2018)
(it <- independence_test(elevel ~ alength, data = alpha,
                         ytrafo = function(data)
                             trafo(data, numeric_trafo = rank_trafo), 
                         xtrafo = function(data)
                             trafo(data, factor_trafo = function(x)

## Extract the "best" set of scores
ss <- statistic(it, type = "standardized")
idx <- which(abs(ss) == max(abs(ss)), arr.ind = TRUE)
ss[idx[1], idx[2], drop = FALSE]

coin documentation built on Sept. 27, 2023, 5:09 p.m.