R/factor.responses.R

In antagomir/netresponse: Functional Network Analysis

# Copyright (C) 2010-2016 Leo Lahti Contact: Leo Lahti <leo.lahti@iki.fi> This
# program is free software; you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2, or (at your option) any later version.  This
# program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.  See the GNU General Public License for more details.

#' @title Factor responses
#' @description List responses for each level of the given factor
#' @param annotation.vector annotation vector with discrete factor levels, and named by the samples
#' @param groupings List of groupings. Each model should have a sample-cluster assignment matrix qofz, or a vector of cluster indices named by the samples.
#' @param method method for enrichment calculation
#' @param min.size minimum sample size for a response 
#' @param data data (samples x features; or a vector in univariate case)
#' @return List with each element corresponding to one factor level and listing the responses according to association strength
#' @author Contact: Leo Lahti \email{leo.lahti@@iki.fi}
#' @references See citation('netresponse')
#' @export
#' @keywords utilities
#' @examples res <- factor.responses(annotation.vector = NULL, groupings = NULL)
factor.responses <- function(annotation.vector, groupings, method = "hypergeometric", 
    min.size = 2, data = NULL) {

    if (is.null(groupings)) {return(NULL)}

    responses <- list()
    
    annotation.vector <- factor(annotation.vector)
    
    levels <- as.character(na.omit(unique(droplevels(annotation.vector))))
    
    for (lev in levels) {
        
        level.samples <- names(annotation.vector)[which(annotation.vector == lev)]
        
        ors <- enrichment.list.factor(groupings, level.samples, method = method)
        
        if (is.null(ors)) {
            ors <- NA
            warning(paste("No significant responses for level", lev))
        }
        
        responses[[as.character(lev)]] <- ors
    }
    
    # Pick top responses for each factor level
    responses <- responses[!is.na(responses)]
    
    responses.per.level <- NULL
    if (length(responses) > 0) {
        
        responses.per.level <- lapply(responses, function(dr) {
            dr$ordered.responses
        })
        responses.per.level <- responses.per.level[sapply(responses.per.level, nrow) > 
            0]
        
    }
    
    responses.per.level
    
}