R/geneEnrich.R

In Bin-Chen-Lab/octad_desktop: Open Cancer TherApeutic Discovery (OCTAD)

#' @export
#' @import httr
geneEnrich=function(gene_list=NULL,database_list=NULL,output=FALSE){

    if(is.null(gene_list)|is.null(database_list)){
        stop('Source gene_list vector and database_list vector please')
    }
    #send a request with gene_list
    gene_list_collapsed=list(list=paste(gene_list,collapse='\n'))
    send=(httr::POST('http://amp.pharm.mssm.edu/Enrichr/addList',body=gene_list_collapsed)) #send a response
    user_list_id = httr::content(send,type='application/json')$userListId #retreive list id
    
    
    
    ###########extract GO data by libraries
    GO_enriched=list()
    
    for (j in database_list){
        
        raw_return=httr::GET(paste0('http://amp.pharm.mssm.edu/Enrichr/enrich?userListId=',user_list_id,'&backgroundType=',j))
        raw_return=httr::content(raw_return,type='application/json') #transform binary to list
        
        
        ################unlist obtained list
        genes=vector() #collapse genes into single field. 
    #some hardcoding stuff to collapse genes into single field or row 30-31 won't work and no parsing for obtained list. 
    # Gene names strickly placed in the [[x]][[y]][6] leaf of list, where [[x]]- name of the database and [[y]] GO entry (eg pathway).
        for (i in 1:length(raw_return[[j]])){
            genes=c(genes,paste(unlist(raw_return[[j]][[i]][6]),collapse=';')) 
            raw_return[[j]][[i]][6]=NULL
        }
        #### end of hardcoding
    
        #transform list to data.frame, rename columns and compute FDR since enlisted protocol does not gives it. WILL NOT WORK WO line 26-29 transformation!
        result_temp=data.frame(matrix(unlist(raw_return[[j]]), 
                                                                    nrow=length(raw_return[[j]]), byrow=TRUE)) 
        colnames(result_temp)= c('Rank', 'Term name', 'P-value', 'Z-score', 'Combined score', 'FDR', 'Old p-value', 'Old adjusted p-value')
        result_temp$genes=genes
#        result_temp$FDR=p.adjust(result_temp$`P-value`,method='fdr')
        
        if(output==TRUE){ #write result to working directory
            write.csv(result_temp,file=paste0(j,'_GO_enrichment.csv'))
        }
        
        GO_enriched[[j]]=result_temp
    } #End of database obtaining
    return(GO_enriched)
} #End of function