Prepare a table annotations for human genes using Bioconductor

merge_bioC_Hs_gene_db.R

# I am sure this can be done in a multiple of ways: but here's a nice example of use of Reduce for merging lists 
# This particular use case if when you are trying to make a look up table for Human genes
# Check out Marc Carlson's Annotationdbi packages and tutorials for alternative ways (SQL) of retrieving the information 
# Caution note:
# the unintended consequence of joining on the Entrez Gene ids is the Ensembl ids for alternative ids are lost and usually the 
# alternative ensembl id is used

# load package from the BioConductor Project
library("org.Hs.eg.db")
library("tidyverse")

Reduce(function(...) merge(..., by='gene_id', all.x=TRUE), 
       list(toTable(org.Hs.egENSEMBL2EG),
            toTable(org.Hs.egSYMBOL),
            toTable(org.Hs.egGENENAME))) %>% 
  as.tibble() 
  
  # A tibble: 28,964 x 4
   gene_id   ensembl_id      symbol     gene_name                                    
   <chr>     <chr>           <chr>      <chr>                                        
 1 1         ENSG00000121410 A1BG       alpha-1-B glycoprotein                       
 2 10        ENSG00000156006 NAT2       N-acetyltransferase 2                        
 3 100       ENSG00000196839 ADA        adenosine deaminase                          
 4 1000      ENSG00000170558 CDH2       cadherin 2                                   
 5 10000     ENSG00000117020 AKT3       AKT serine/threonine kinase 3                
 6 10000     ENSG00000275199 AKT3       AKT serine/threonine kinase 3                
 7 100008586 ENSG00000236362 GAGE12F    G antigen 12F