R/geneAnswersReadable.R

In GeneAnswers: Integrated Interpretation of Genes

`geneAnswersReadable` <-
function(x, catTerm=TRUE, geneSymbol=TRUE, strict=FALSE, verbose=TRUE, missing=c('name', 'keep', 'remove'), ...) {
	missing <- match.arg(missing)
	y <- x
	if (geneSymbol) {
		if (verbose) print('Mapping geneInput ...')
		y@geneInput[,1] <- getSymbols(as.vector(x@geneInput[,1]), x@annLib, strict=strict, missing=missing)		
	}
 	if (verbose) print('Mapping genesInCategory ...')
	if (geneSymbol) y@genesInCategory <- lapply(x@genesInCategory, getSymbols, x@annLib, strict=strict, missing=missing)
	if (catTerm) names(y@genesInCategory) <- getCategoryTerms(names(x@genesInCategory), x@categoryType, strict=strict, missing=missing, ...)
	if (catTerm) {
		if (verbose) print('Mapping enrichmentInfo rownames ...')
		rownames(y@enrichmentInfo) <- getCategoryTerms(rownames(x@enrichmentInfo), x@categoryType, strict=strict, missing=missing, ...)
	}
	if (!is.null(y@geneExprProfile) & geneSymbol) {
		if (verbose) print('Mapping geneExprProfile rownames ...')
		y@geneExprProfile <- cbind(getSymbols(as.character(x@geneExprProfile[,1]), x@annLib, strict=strict, missing=missing), x@geneExprProfile[,2:dim(x@geneExprProfile)[2]])
		colnames(y@geneExprProfile)  <- colnames(x@geneExprProfile)
	}
	return(y)
}