Rserve and the R plugin for PLINK - ohsu-comp-bio/cedar-gwas GitHub Wiki

Install Rserve (using R cmd prompt):

install.packages("Rserve")

Run Rserve daemon:

R CMD Rserve

Example function:

     Rplink <- function(PHENO,GENO,CLUSTER,COVAR)
     {
       f1 <- function(s) 
       {
        m <- glm( PHENO ~ s , family="binomial" )
        r <- summary(m)$coef[8]
        c( length(r) , r )
       }
      apply( GENO , 2 , f1 )
     }

Running R-plugin with custom function:

plink --file mydata --R myscript.R