Import NCBI (Entrez) gene identifier information
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.- refseqGeneSummary
logical(1). Include RefSeq gene summary in"refseqGeneSummary"column. Requires Bioconductor GeneSummary package to be installed.
Examples
object <- NcbiGeneInfo(
organism = "Homo sapiens",
taxonomicGroup = "Mammalia"
)
#> → Downloading Homo sapiens gene info from NCBI at <https://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz>.
#> → Caching URL at <https://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz> into /private/var/folders/pt/1g5629f1699dfjwdfh32q50m0000gn/T/koopa-r-docs-build-l3dklp41/home/.cache/R/AcidGenomes/BiocFileCache.
#>
#> → Importing /private/var/folders/pt/1g5629f1699dfjwdfh32q50m0000gn/T/koopa-r-docs-build-l3dklp41/home/.cache/R/AcidGenomes/BiocFileCache/a36547c18b02_Homo_sapiens.gene_info.gz using base::`read.table()`.
print(object)
#> NcbiGeneInfo with 193911 rows and 13 columns
#> chromosome
#> <character>
#> 1 19
#> 2 12
#> 9 8
#> 10 8
#> 11 8
#> ... ...
#> 8923215 MT
#> 8923216 MT
#> 8923217 MT
#> 8923218 MT
#> 8923219 MT
#> dbXrefs
#> <CharacterList>
#> 1 AllianceGenome:HGNC:5,Ensembl:ENSG00000121..,HGNC:HGNC:5,...
#> 2 AllianceGenome:HGNC:7,Ensembl:ENSG00000175..,HGNC:HGNC:7,...
#> 9 AllianceGenome:HGNC:..,Ensembl:ENSG00000171..,HGNC:HGNC:7645,...
#> 10 AllianceGenome:HGNC:..,Ensembl:ENSG00000156..,HGNC:HGNC:7646,...
#> 11 AllianceGenome:HGNC:15,HGNC:HGNC:15
#> ... ...
#> 8923215
#> 8923216
#> 8923217
#> 8923218
#> 8923219
#> description featureType geneId geneName
#> <character> <character> <integer> <character>
#> 1 alpha-1-B glycoprotein NA 1 A1BG
#> 2 alpha-2-macroglobulin NA 2 A2M
#> 9 N-acetyltransferase 1 NA 9 NAT1
#> 10 N-acetyltransferase 2 NA 10 NAT2
#> 11 N-acetyltransferase .. NA 11 NATP
#> ... ... ... ... ...
#> 8923215 tRNA-Asp NA 8923215 trnD
#> 8923216 tRNA-Pro NA 8923216 trnP
#> 8923217 tRNA-Ala NA 8923217 trnA
#> 8923218 cytochrome c oxidase.. NA 8923218 COX1
#> 8923219 l-rRNA NA 8923219 16S rRNA
#> geneSynonyms mapLocation modificationDate nomenclatureStatus
#> <CharacterList> <character> <Date> <character>
#> 1 A1B,ABG,GAB,... 19q13.43 2026-09-10 O
#> 2 A2MD,CPAMD5,FWP007,... 12p13.31 2026-09-13 O
#> 9 AAC1,MNAT,NAT-1,... 8p22 2026-09-20 O
#> 10 AAC2,NAT-2,PNAT 8p22 2026-09-10 O
#> 11 AACP,NATP1 8p22 2026-05-19 O
#> ... ... ... ... ...
#> 8923215 NA 2020-09-09 NA
#> 8923216 NA 2020-09-09 NA
#> 8923217 NA 2020-09-09 NA
#> 8923218 NA 2026-06-16 NA
#> 8923219 NA 2020-09-09 NA
#> otherDesignations
#> <CharacterList>
#> 1 HEL-S-163pA,alpha-1B-glycoprotein,epididymis secretory..
#> 2 C3 and PZP-like alph..,alpha-2-M,alpha-2-macroglobulin
#> 9 N-acetyltransferase ..,N-acetyltransferase ..,N-hydroxyarylamine O..,...
#> 10 N-acetyltransferase ..,N-acetyltransferase ..,N-hydroxyarylamine O..,...
#> 11 arylamide acetylase ..
#> ... ...
#> 8923215
#> 8923216
#> 8923217
#> 8923218 cytochrome c oxidase..
#> 8923219
#> taxonomyId typeOfGene
#> <integer> <character>
#> 1 9606 protein-coding
#> 2 9606 protein-coding
#> 9 9606 protein-coding
#> 10 9606 protein-coding
#> 11 9606 pseudo
#> ... ... ...
#> 8923215 741158 tRNA
#> 8923216 741158 tRNA
#> 8923217 741158 tRNA
#> 8923218 741158 protein-coding
#> 8923219 741158 rRNA