R/alias2Symbol.R

In hdeberg/limma: Linear Models for Microarray Data

##  ALIAS2SYMBOL.R

alias2Symbol <- function(alias,species="Hs",expand.symbols=FALSE)
#  Convert a set of alias names to official gene symbols
#  via Entrez Gene identifiers
#  Di Wu, Gordon Smyth and Yifang Hu
#  4 Sep 2008. Last revised 23 June 2016.
{
	alias <- as.character(alias)

#	Get access to required annotation functions
	suppressPackageStartupMessages(OK <- requireNamespace("AnnotationDbi",quietly=TRUE))
	if(!OK) stop("AnnotationDbi package required but is not installed (or can't be loaded)")

#	Load appropriate organism package
	orgPkg <- paste0("org.",species,".eg.db")
	suppressPackageStartupMessages(OK <- requireNamespace(orgPkg,quietly=TRUE))
	if(!OK) stop(orgPkg," package required but is not installed (or can't be loaded)")

#	Get alias to Entrez Gene mappings
	obj <- paste0("org.",species,".egALIAS2EG")
	egALIAS2EG <- tryCatch(getFromNamespace(obj,orgPkg), error=function(e) FALSE)
	if(is.logical(egALIAS2EG)) stop("Can't find alias mappings in package ",orgPkg)

#	Get symbol to Entrez Gene mappings
	obj <- paste0("org.",species,".egSYMBOL")
	egSYMBOL <- tryCatch(getFromNamespace(obj,orgPkg), error=function(e) FALSE)
	if(is.logical(egSYMBOL)) stop("Can't find symbol mappings in package ",orgPkg)

	if(expand.symbols) {
		alias <- intersect(alias,AnnotationDbi::Rkeys(egALIAS2EG))
		eg <- AnnotationDbi::mappedLkeys(egALIAS2EG[alias])
		AnnotationDbi::mappedRkeys(egSYMBOL[eg])
	} else {
		isSymbol <- alias %in% AnnotationDbi::Rkeys(egSYMBOL) 
		alias2 <- intersect(alias[!isSymbol],AnnotationDbi::Rkeys(egALIAS2EG))
		eg <- AnnotationDbi::mappedLkeys(egALIAS2EG[alias2])
		c(alias[isSymbol],AnnotationDbi::mappedRkeys(egSYMBOL[eg]))
	}
}

alias2SymbolTable <- function(alias,species="Hs")
#  Convert a vector of alias names to the vector of corresponding official gene symbols
#  via Entrez Gene identifiers
#  Di Wu, Gordon Smyth and Yifang Hu
#  Created 3 Sep 2009.  Last modified 23 April 2016.
{
	alias <- as.character(alias)

#	Get access to required annotation functions
	suppressPackageStartupMessages(OK <- requireNamespace("AnnotationDbi",quietly=TRUE))
	if(!OK) stop("AnnotationDbi package required but is not installed (or can't be loaded)")

#	Load appropriate organism package
	orgPkg <- paste0("org.",species,".eg.db")
	suppressPackageStartupMessages(OK <- requireNamespace(orgPkg,quietly=TRUE))
	if(!OK) stop(orgPkg," package required but is not installed (or can't be loaded)")

#	Get alias to Entrez Gene mappings
	obj <- paste0("org.",species,".egALIAS2EG")
	egALIAS2EG <- tryCatch(getFromNamespace(obj,orgPkg), error=function(e) FALSE)
	if(is.logical(egALIAS2EG)) stop("Can't find alias mappings in package ",orgPkg)

#	Get symbol to Entrez Gene mappings
	obj <- paste0("org.",species,".egSYMBOL")
	egSYMBOL <- tryCatch(getFromNamespace(obj,orgPkg), error=function(e) FALSE)
	if(is.logical(egSYMBOL)) stop("Can't find symbol mappings in package ",orgPkg)

#	Output vector same length as input
	Symbol <- alias

#	Check which aliases are already symbols
	isSymbol <- alias %in% AnnotationDbi::Rkeys(egSYMBOL)
	Symbol[!isSymbol] <- NA

#	Now deal with rest
	OtherAliases <- alias[!isSymbol]
	isAlias <- OtherAliases %in% AnnotationDbi::Rkeys(egALIAS2EG)
	if(!any(isAlias)) return(Symbol)
	OtherAliases <- OtherAliases[isAlias]
	AliasTbl <- AnnotationDbi::toTable(egALIAS2EG[OtherAliases])
	if(anyDuplicated(AliasTbl$alias_symbol)) warning("Multiple symbols ignored for one or more aliases")
	SymbolTbl <- AnnotationDbi::toTable(egSYMBOL[AliasTbl$gene_id])
	m <- match(OtherAliases,AliasTbl$alias_symbol)
	GeneID <- AliasTbl$gene_id[m]
	m <- match(GeneID,SymbolTbl$gene_id)
	Symbol[!isSymbol][isAlias] <- SymbolTbl$symbol[m]

	Symbol
}

alias2SymbolUsingNCBI <- function(alias,gene.info.file,required.columns=c("GeneID","Symbol","description"))
#	Convert gene aliases to current symbols etc using a gene_info file downloaded from the NCBI
#	Gordon Smyth
#	Created 2 March 2017. Last modified 9 June 2020.
{
#	Check input. If necessary, read the gene info file.
	alias <- as.character(alias)
	if(is.data.frame(gene.info.file)) {
		OK <- all(c("GeneID","Symbol","Synonyms") %in% names(gene.info.file))
		if(!OK) stop("The gene.info.file must include columns GeneID, Symbol and Synonyms")
		NCBI <- gene.info.file
		NCBI$Symbol <- as.character(NCBI$Symbol)
	} else {
		gene.info.file <- as.character(gene.info.file)
    	NCBI <- read.delim(gene.info.file,comment.char="",quote="",colClasses="character")
    }

#	Try matching to symbols
	m <- match(alias,NCBI$Symbol)
	EntrezID <- NCBI$GeneID[m]

#	For any rows that don't match symbols, try synonyms
	i <- which(is.na(EntrezID))
	if(any(i)) {
		S <- strsplit(NCBI$Synonyms,split="\\|")
		N <- vapply(S,length,1)
		Index <- rep.int(1:nrow(NCBI),times=N)
		IS <- data.frame(Index=Index,Synonym=unlist(S),stringsAsFactors=FALSE)
		m <- match(alias[i],IS$Synonym)
		EntrezID[i] <- NCBI$GeneID[IS$Index[m]]
		m <- match(EntrezID,NCBI$GeneID)
    }

    NCBI[m,required.columns,drop=FALSE]
}