#' Sphere of Influence Step
#'
#' Sphere of Influence assesses if a
#' candidate gene i meets the first criterion by testing if gene i
#' is more strongly correlated with its network neighbors than with a
#' random set of genes
#'
#' @param gene.id The name of the gene to which GeneSurrounder is applied
#' @param distance.matrix A matrix of the distances on the global network
#' @param cor.matrix A matrix of correlations between the expression of the genes
#' @param diameter The diameter of the global network
#' @param genes.assayedETnetwork The names of the genes that are assayed and on the network
#'
Observed.SI <- function(gene.id,
distance.matrix,
cor.matrix,
diameter,
genes.assayedETnetwork){
# Vector of cor between j and all other genes on network (excluding j)
cor.with.j <- cor.matrix[gene.id,
setdiff(genes.assayedETnetwork,gene.id)]
distances.to.j <- distance.matrix[gene.id,
setdiff(genes.assayedETnetwork,gene.id)]
observed.cor <- SumAbsCor(cor.with.j,
diameter,
distances.to.j)
}
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