R/utils.R

In CEMiTool: Co-expression Modules identification Tool

get_forced_beta <- function(cem, network_type){
    num_samples <- ncol(expr_data(cem))
    num_tests <- c(20, 30, 40, 60)
    if(network_type=="unsigned"){
        beta_values <- c(9, 8, 7, 6)
        if(num_samples < 20){
            beta <- 10
        }else{
            beta <- beta_values[which(num_tests == max(num_tests[num_tests <= num_samples]))]
        }
    }else if(network_type=="signed"){
        beta_values <- c(18, 16, 14, 12)
        if(num_samples < 20){
            beta <- 20
        }else{
            beta <- beta_values[which(num_tests == max(num_tests[num_tests <= num_samples]))]
        }
    }
    return(beta)
}

get_args <- function(cem, vars){
    system_calls <- lapply(sys.calls(), as.character)
    go_back <- ifelse(".local" %in% unlist(system_calls), 2, 1)

    # Get function name
    func <- as.character(sys.calls()[[sys.nframe()-go_back]][[1]])

    # Get command
    if(class(get(func)) == "function"){
        command <- deparse(sys.call(-1))
    }else if(class(get(func)) == "nonstandardGenericFunction"){
        command <- deparse(sys.call(-2))
    }

    # Get the name of the cemitool object variable
    cem_name <- names(vars[sapply(vars, class) == "CEMiTool"])

    # Create input_params slot
    exceptions <- c("expr", "sample_annot", "gmt", "interactions", "value")
    vars[["cem"]] <- NULL
    vars[["results"]] <- NULL
    vars[names(vars) %in% exceptions] <- "input"
    inputs <- cem@input_params
    inputs[[func]] <- vars
    cem@input_params <- inputs
    
    # Create calls slot
    calls <- cem@calls

    ## Deal with setter functions
    setters <- c("expr_data<-", "sample_annotation<-", "interactions_data<-")
    test_command <- sapply(setters, function(f) grepl(f, command[[1]], fixed=TRUE))
    if(sum(test_command) > 0){
        f <- names(which(test_command))
        sub <- paste0("(", cem_name, ") <-")
        f <- gsub("<-", sub, f)
        command <- paste(f, "input")
    }

    calls[[length(calls) + 1]] <- command
    if(length(calls) == 1){
        names(calls) <- func
    }else{
        names(calls)[length(calls)] <- func
    }

    cem@calls <- calls
    return(cem)
}

stop_if <- function (expr, error) {
        if (expr) stop(error, call. = FALSE)
}

flip_vector <- function(x){
        return(setNames(names(x), x))
}