R/mat2adj.R

In filosi/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, infer.method='cor', use='all.obs', ...){

    METHODS <- c('cor','WGCNA','WGCNAFDR','bicor',
                 'bicorFDR','TOM','ARACNE','CLR',
                 'MINE','MINEFDR','DTWMIC', 'c3net',
                 'bc3net')
    MEASURE <- c('MIC','MAS','MCN','MEV','MICR2')
    infer.method <- pmatch(infer.method, METHODS)
    if(is.na(infer.method))
        stop("invalid distance method", call. = FALSE)
    if(infer.method == -1)
        stop("ambiguous distance method", call. = FALSE)
    ## Uncomment the following to restore
    ## 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[infer.method],sep='')
        tmp <- do.call(myfun, args=list(x=x, ...))
        return(tmp)
    }
}
setMethod("mat2adj","matrix",mat2adj.matrix)