Import NCBI Entrez gene identifier information

EntrezGeneInfo(organism, taxonomicGroup = NULL)

Arguments

organism

character(1). Full Latin organism name (e.g. "Homo sapiens").

taxonomicGroup

character(1). NCBI FTP server taxonomic group subdirectory path (e.g. "Mammalia"). Defining this manually avoids having to query the FTP server.

Value

EntrezGeneInfo.

Note

Updated 2021-02-25.

See also

Examples

object <- EntrezGeneInfo( organism = "Homo sapiens", taxonomicGroup = "Mammalia" )
#> → Downloading Homo sapiens gene info from NCBI at <ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz>.
#> → Importing af13430a6cd5_Homo_sapiens.gene_info.gz at /opt/koopa/opt/r/cache/AcidGenomes using data.table::`fread()`.
print(object)
#> EntrezGeneInfo with 61757 rows and 13 columns #> chromosome dbXrefs #> <Rle> <CharacterList> #> 1 19 Ensembl:ENSG00000121..,HGNC:HGNC:5,MIM:138670 #> 2 12 Ensembl:ENSG00000175..,HGNC:HGNC:7,MIM:103950 #> 3 12 Ensembl:ENSG00000256..,HGNC:HGNC:8 #> 9 8 Ensembl:ENSG00000171..,HGNC:HGNC:7645,MIM:108345 #> 10 8 Ensembl:ENSG00000156..,HGNC:HGNC:7646,MIM:612182 #> ... ... ... #> 8923215 MT #> 8923216 MT #> 8923217 MT #> 8923218 MT #> 8923219 MT #> description featureType geneId geneName #> <Rle> <Rle> <Rle> <Rle> #> 1 alpha-1-B glycoprotein NA 1 A1BG #> 2 alpha-2-macroglobulin NA 2 A2M #> 3 alpha-2-macroglobuli.. NA 3 A2MP1 #> 9 N-acetyltransferase 1 NA 9 NAT1 #> 10 N-acetyltransferase 2 NA 10 NAT2 #> ... ... ... ... ... #> 8923215 tRNA NA 8923215 trnD #> 8923216 tRNA NA 8923216 trnP #> 8923217 tRNA NA 8923217 trnA #> 8923218 cytochrome c oxidase.. NA 8923218 COX1 #> 8923219 l-rRNA NA 8923219 16S rRNA #> geneSynonyms mapLocation modificationDate nomenclatureStatus #> <CharacterList> <Rle> <Rle> <Rle> #> 1 A1B,ABG,GAB,... 19q13.43 20210129 O #> 2 A2MD,CPAMD5,FWP007,... 12p13.31 20210129 O #> 3 A2MP 12p13.31 20210129 O #> 9 AAC1,MNAT,NAT-1,... 8p22 20210129 O #> 10 AAC2,NAT-2,PNAT 8p22 20210129 O #> ... ... ... ... ... #> 8923215 NA 20200909 NA #> 8923216 NA 20200909 NA #> 8923217 NA 20200909 NA #> 8923218 NA 20200909 NA #> 8923219 NA 20200909 NA #> otherDesignations #> <CharacterList> #> 1 alpha-1B-glycoprotein,epididymis secretory..,HEL-S-163pA #> 2 alpha-2-M,alpha-2-macroglobulin,C3 and PZP-like alph.. #> 3 pregnancy-zone prote.. #> 9 arylamide acetylase 1,arylamine N-acetyltr..,monomorphic arylamin..,... #> 10 arylamide acetylase 2,arylamine N-acetyltr..,N-acetyltransferase ..,... #> ... ... #> 8923215 #> 8923216 #> 8923217 #> 8923218 cytochrome c oxidase.. #> 8923219 #> typeOfGene xTaxId #> <Rle> <Rle> #> 1 protein-coding 9606 #> 2 protein-coding 9606 #> 3 pseudo 9606 #> 9 protein-coding 9606 #> 10 protein-coding 9606 #> ... ... ... #> 8923215 tRNA 741158 #> 8923216 tRNA 741158 #> 8923217 tRNA 741158 #> 8923218 protein-coding 741158 #> 8923219 rRNA 741158