conditional testing of SNPs - reports number and which SNPs are "significant" in sequential conditional testing

cond.R

library(snpStats)
  best <- cond.best(X,Y, family=family)
  while(length(newbest <- cond.best(X, Y, best, family=family)))
    best <- c(best,newbest)

cond.best <- function(X,Y,best=NULL,p.thr=1e-6, ...) {
  if(is.null(best)) {
    cond <- snp.rhs.tests(Y ~ 1, snp.data=X, data=data.frame(Y=Y,
row.names=rownames(X)), ...)
    p.thr <- 1
  } else {
    cond <- snp.rhs.tests(as.formula(paste("Y ~", paste(best, collapse="+"))),
                          snp.data=X,
                          data=cbind(data.frame(Y=Y,row.names=rownames(X)),as(X[,best],"numeric")), 
                          control=glm.test.control(R2Max=1), 
                          ...)
  }
  p <- p.value(cond)
  pmin <- min(p, na.rm=TRUE)
  if(pmin<p.thr) {
    newbest <- colnames(X)[ which.min(p) ]
    message(newbest," ",format.pval(pmin))
    return(newbest)
  }
  return(NULL)
}