R/update_how.R

In ceRNAnetsim: Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

#' Converts the count value of the given node.
#'
#' this function converts the count value of the given node.
#'
#' @importFrom igraph E 'E<-'
#' @return the graph object.
#'
#' @details update_how function calculates the current value of
#' given mirna or gene node on the graph object. User must specify
#' current value as fold change.
#'
#' @param input_graph The graph object that processed in previous step/s.
#' @param node_name The name of the node whose count is to be changed.
#' @param how The change in terms of fold change.
#' @param knockdown specifies gene knockdown with default TRUE
#'
#' @examples
#'
#' data('minsamp')
#'
#' priming_graph(minsamp, Competing_expression, miRNA_expression)%>%
#'    update_how('Gene1',3)
#'
#'  priming_graph(minsamp, Competing_expression, miRNA_expression,
#'       aff_factor = c(seed_type,energy), deg_factor = region)%>%
#'    update_how('Gene1', 3)
#'
#'    priming_graph(minsamp, Competing_expression, miRNA_expression,
#'        aff_factor = c(seed_type,energy), deg_factor = region)%>%
#'   update_how('Gene1', how=0, knockdown= TRUE)
#'
#'
#'
#' @export

update_how <- function(input_graph, node_name, how, knockdown = TRUE) {

  if (how < 0)
    stop("Fold change should not be less than zero.
                     Please use decimal values for decrease. e.g. 0.5 for 2-fold decrease",
         call. = FALSE)

  if (how == 0 & knockdown) {

    return(input_graph %>% gene_knockdown(node_name) %>% update_nodes())
  }

  if (node_name %in% E(input_graph)$Competing_name) {

    input_graph <- input_graph %>% tidygraph::activate(edges) %>% tidygraph::mutate(comp_count_current = ifelse(node_name ==
                                                                                                                  E(input_graph)$Competing_name, comp_count_current * how, comp_count_current))

  } else if (node_name %in% E(input_graph)$miRNA_name) {

    input_graph <- input_graph %>% tidygraph::activate(edges) %>% tidygraph::mutate(mirna_count_current = ifelse(node_name ==
                                                                                                                   E(input_graph)$miRNA_name, mirna_count_current * how, mirna_count_current))

  } else {

    stop(paste("Given node name", node_name, "was not found! Please check it.",
               sep = " "))

  }

  return(input_graph %>% update_nodes())
}



#' Knocks down given node.
#'
#' @importFrom igraph E
#' @return the graph object.
#'
#' @details knocks down a given gene target.
#'
#' @param input_graph The graph object that processed in previous step/s.
#' @param node_name The name of the node whose count is to be knocked down.
#'
#' @keywords internal
#'

gene_knockdown <- function(input_graph, node_name) {

  input_graph <- input_graph %>% tidygraph::activate(edges) %>% tidygraph::mutate(comp_count_current = ifelse(node_name ==
                                                                                                                E(input_graph)$Competing_name, 0, comp_count_current))

  return(input_graph %>% update_nodes())

}