R/run_bc3net.R

In tgrimes/dnapath2: Differential Network Analysis Using Gene Pathways

# install.packages("bc3net")


#' Wrapper for BC3Net method
#' 
#' Conducts co-expression analysis using BC3Net
#' @param x The n by p matrix of counts.
#' @return A p by p matrix of association scores.
#' @export
run_bc3net <- function(x, method = "spearman", alpha = 0.05, ...) {
  scores <- bc3net::bc3net(t(x), alpha1 = alpha, alpha2 = alpha, 
                           estimator = method, igraph = FALSE)
  
  colnames(scores) <- colnames(x)
  rownames(scores) <- NULL
  
  return(scores)
}