inference-of-GRN-using-Fused-LASSO

Gene regulatory network inference using fused LASSO on multiple data sets: application to Escherichia coli

To run the program with the introduced data in the article, you only need to do as follows:

1- Run R

2- library(lqa)

3- trace(fused.lasso,edit=T)

4- substitute the existing function with the function in fused.lasso.modified.r (following function):

function (lambda = NULL, ...) 					
{					
  argList = list(...)					
  w <- argList$...					
  lambda.check(lambda)					
  if (length(lambda) != 2) 					
    stop("The fused.lasso penalty must consist on two parameters! \n")					
  names(lambda) <- c("lambda1", "lambda2")					
  first.derivative <- function(beta = NULL, ...) {					
    if (is.null(beta)) 					
      stop("'beta' must be the current coefficient vector \n")					
    p <- length(beta)					
    if (p < 2) 					
      stop("There must be at least two regressors! \n")					
    vec1 <- c(rep(lambda[1], p), rep(lambda[2], (3/4) * p))					
    vec2 <- abs(drop(t(a.coefs(beta, ... = w)) %*% beta))					
    #print(any(vec2 < 0))					
    return(vec1 * vec2)					
  }					
  a.coefs <- function(beta = NULL, ...) {					
    argList = list(...)					
    w <- argList$...					
    if (is.null(beta)) 					
      stop("'beta' must be the current coefficient vector \n")					
    p <- length(beta)					
    if (p < 2) 					
      stop("There must be at least two regressors! \n")					
    if (p > 2) {					
      h1 <- cbind(-diag((3/4) * p), matrix(0, (3/4) * p, (1/4) * p))					
      h2 <- cbind(matrix(0, (3/4) * p, (1/4) * p), diag((3/4) * p))					
      #print("i did it :)")					
      mat1 <- h1 + h2					
      mat2 <- diag(w)					
      a.coefs.mat <- cbind(mat2, t(mat1))					
    }					
    else a.coefs.mat <- cbind(diag(2), c(-1, 1))					
    return(a.coefs.mat)					
  }					
  structure(list(penalty = "fused.lasso", lambda = lambda, 					
	         first.derivative = first.derivative, a.coefs = a.coefs), 				
	    class = "penalty")				
}					

5- source("sources.r") #make sure that source.r is in the correct directory