R/gene76.R

In genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

if(getRversion() >= "2.15.1")  utils::globalVariables("sig.gene76")

`gene76` <-
function(data, er) {
	
	A <- 313.5
	B <- 280

	if (length(intersect(colnames(data), sig.gene76$EntrezGene.ID)) < 1) {
		warning('No overlap between the column names of data and the ',
			'EntrezGene.IDs in the sig.gene76 object. Please ensure one ',
			'or more of the gene signature genes are in your data! ',
			'Returning NAs.')
		return(list('score'=NA, 'risk'=NA))
	}

	score <- NULL
	for(i in 1:nrow(data)) {
		if(is.na(er[i])) { score <- c(score, NA) }
		else {
			if(er[i] == 1) {
				score <- c(score, A + sum(data[i, dimnames(sig.gene76)[[1]][sig.gene76[ ,"er"] == 1]] * sig.gene76[sig.gene76[ ,"er"] == 1,"std.cox.coefficient"]))
			}
			else {
				score <- c(score, B + sum(data[i,dimnames(sig.gene76)[[1]][sig.gene76[ ,"er"] == 0]] * sig.gene76[sig.gene76[ ,"er"] == 0,"std.cox.coefficient"]))
			}
		}
	}
	names(score) <- dimnames(data)[[1]]
	risk <- ifelse(score >= 0, 1, 0)	
	
	return(list("score"=score, "risk"=risk))
}