intermediate

intermediate is R package for eQTl/pQTL mediation analysis.

Installation

You can install intermediate directly from Github using devtools package:

    # install.packages("devtools")
    devtools::install_github("simecek/intermediate")

Example

  # DOQTL liver protein expresion dataset
  data(Tmem68)
  
  # Let us mediate Tmem68 to other proteins
  med <- mediation.scan(target = Tmem68$target,
                        mediator = Tmem68$mediator,
                        annotation = Tmem68$annotation,
                        covar = Tmem68$covar,
                        qtl.geno = Tmem68$qtl.geno)
                        
  # Plot mediation results and identify the mediator                      
  plot(med)                        
  identify(med)
  
  # Interactive plot
  kplot(med)

References

Joel M. Chick, Steven C. Munger, Petr Simecek, Edward L. Huttlin, Kwangbom Choi, Daniel M. Gatti, Narayanan Raghupathy, Karen L. Svenson, Gary A. Churchill & Steven P. Gygi: "Defining the consequences of genetic variation on a proteome-wide scale", Nature (2016) doi:10.1038/nature18270