#### convert gene ID

#author: Zhilin long

#time: 2021.1.19

#'@author Zhilin Long

#'@param gene Character vector, ID vector to be converted

#'@param fromType Character vector, initial ID type

#'@param toType Character vector, ID type to be converted

#'

#'@return data.frame has removed duplication and NA, and can be used directly

IDConvert <- function(genes, 

                       method = c("clusterProfiler", "org.Hs.eg.db"),

                       fromType = c("ENTREZID", "SYMBOL", "ENSEMBL"), 

                       toType = c("ENTREZID", "SYMBOL", "ENSEMBL")

                       ){

    require(org.Hs.eg.db)

    require(clusterProfiler)

    method <- match.arg(method)

    fromType <- match.arg(fromType)

    toType <- match.arg(toType)

    if(method == "clusterProfiler"){

        gene.df <- bitr(genes, fromType = fromType, toType = toType, OrgDb = "org.Hs.eg.db")

        #By default, IDs that are not mapped will be filtered, that is, the entries will be reduced

    }else{

        gene.df <- mapIds(org.Hs.eg.db, 

                          keys = genes, 

                          column = toType, 

                          keytype = fromType,

                          multiVals="first")

        gene.df <- data.frame(ENSEMBL = names(gene.df), SYMBOL = gene.df)

        colnames(gene.df) <- c(fromType, toType)

        # If there is no map, it is NA, that is, the entry remains unchanged

        gene.df <- na.omit(gene.df) 

    }

    #remove duplicates

    gene.df <- gene.df[!duplicated(gene.df[,2]),]

    gene.df <- gene.df[!duplicated(gene.df[,1]),]

    return(gene.df)

}