R/mat2adj.R

In nettools: A Network Comparison Framework

## Compute the adjacency matrix with multiple methods on a N x P matrix (x)
## x =

mat2adj <- function(x,...) UseMethod("mat2adj")

mat2adj.data.frame <- function(x,...){
  x <- apply(x,2,as.numeric)
  x <- as.matrix(x)
  mat2adj(x,...)
}
setMethod("mat2adj","data.frame",mat2adj.data.frame)

mat2adj.matrix <- function(x,method='cor',FDR=1e-3,P=6,measure=NULL,alpha=0.6,C=15,DP=1,...){

  METHODS <- c('cor','WGCNA','WGCNAFDR','bicor',
               'bicorFDR','TOM','ARACNE','CLR',
               'MINE','MINEFDR','DTWMIC')
  MEASURE <- c('MIC','MAS','MCN','MEV','MICR2')
  method <- pmatch(method, METHODS)
  if(is.na(method))
    stop("invalid distance method", call. = FALSE)
  if(method == -1)
    stop("ambiguous distance method", call. = FALSE)
  if(method == 3L)
    if (P > 1){
      P <- 1
      warning("Using WGCNAFDR method with P > 1, not yet implemented,\n P will be ignored")
    }
  ## If mine suite is require, choose the metric
  if (!is.null(measure) && (method < 9L || method > 10L)) {
    method <- 9L
    warning(paste("No method selected for measure",measure,"; MINE will be used"), call.=FALSE)
  }
  
  if (method >= 9L && method <= 10L) {
    measure <- pmatch(measure,MEASURE)
    if (length(measure) == 0){
      measure <- 1L
      warning(paste("No measure selected for method",METHODS[method],"; MIC will be used"), call. = FALSE)
    }
  }
  
  tmp <- checkvar(x,...)
  if(!is.null(tmp)){
    warning(paste("The variables indexed as",paste(tmp,collapse=", "), 
                  "have nearly zero variance: check the data matrix provided or change the tollerance parameter"),
            call.=FALSE) 
    return(NULL)
  } else {
    myfun <- paste('Adj',METHODS[method],sep='')
    tmp <- do.call(myfun,list(x=x,FDR=FDR,P=P,measure=MEASURE[measure],alpha=alpha,C=C,DP=DP,...))
    return(tmp)
  }
}
setMethod("mat2adj","matrix",mat2adj.matrix)