人类基因id转换的R包：GeoTcgaData

一个非常全的人类基因id转换工具

​ GeoTcgaData包中有一个id转换的函数：id_conversion_vector() , 它可以对人类的各种基因id进行转换。2019年9月第一次发布，目前这个包在CRAN的下载量为1633次：

>  dlstats::cran_stats("GeoTcgaData")
       start        end downloads     package
1 2019-09-01 2019-09-30       412 GeoTcgaData
2 2019-10-01 2019-10-31       168 GeoTcgaData
3 2019-11-01 2019-11-30       204 GeoTcgaData
4 2019-12-01 2019-12-31       206 GeoTcgaData
5 2020-01-01 2020-01-31       441 GeoTcgaData
6 2020-02-01 2020-02-24       202 GeoTcgaData
> sum(dlstats::cran_stats("GeoTcgaData")$downloads)
[1] 1633

2020年2月20日我在github和CRAN上对它进行了更新，支持转换的id种类更多！同时它对基因id的转换率也很不错。

小提示：在家里我发现用电脑从github上安装R包会很慢，但是用电脑连接手机热点却可以比较轻松的安装github上的R包。

GeoTcgaData的安装方法为：

从github上安装开发中的版本：

if(!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("huerqiang/GeoTcgaData")

如果电脑上没有安装devtools，也可以使用remotes来安装github上的包。remotes包比devtools小的多，也更好安装。

if(!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("huerqiang/GeoTcgaData")

或者从CRAN上安装稳定版

install.packages("GeoTcgaData")

它所支持的id种类为：

id_ava()

[1] "hgnc_id"                  "symbol"                   "name"                     "locus_group"              "locus_type"               "status"                  
[7] "location"                 "location_sortable"        "prev_name"                "gene_family"              "gene_family_id"           "date_approved_reserved"  
[13] "date_symbol_changed"      "date_name_changed"        "date_modified"            "entrez_id"                "ensembl_gene_id"          "vega_id"                 
[19] "ucsc_id"                  "ena"                      "refseq_accession"         "ccds_id"                  "uniprot_ids"              "pubmed_id"               
[25] "mgd_id"                   "rgd_id"                   "cosmic"                   "omim_id"                  "mirbase"                  "homeodb"                 
[31] "snornabase"               "bioparadigms_slc"         "orphanet"                 "pseudogene.org"           "horde_id"                 "merops"                  
[37] "imgt"                     "iuphar"                   "kznf_gene_catalog"        "mamit-trnadb"             "cd"                       "lncrnadb"                
[43] "enzyme_id"                "intermediate_filament_db" "rna_central_ids"          "lncipedia"                "gtrnadb"                  "NCBI Gene ID" 

使用方法如下：

genes <- c("A2ML1", "A2ML1-AS1", "A4GALT", "OR52L1", "AAAS")
#从gene symbol转到 Ensembl ID
ense <- id_conversion_vector("symbol", "ensembl_gene_id", genes) 
ense

[1] "ENSG00000166535" "ENSG00000256661" "ENSG00000128274" "ENSG00000183313" "ENSG00000094914"

#从Ensembl ID 转到 uniprot id
uni <- id_conversion_vector("ensembl_gene_id", "uniprot_ids", ense) 
#从Ensembl ID 转到 entrez id
ent <- id_conversion_vector("ensembl_gene_id", "entrez_id", ense) 
uni
ent

[1] "A8K2U0" ""       "Q9NPC4" "Q8NGH7" "Q9NRG9"
[1] "   144568" "100874108" "    53947" "   338751" "     8086"

此外，我们也可以查看基因的全称等。

genes <- c("A2ML1", "A2ML1-AS1", "A4GALT", "OR52L1", "AAAS")
id_conversion_vector("symbol", "name", genes) 

[1] "alpha-2-macroglobulin like 1"                                        "A2ML1 antisense RNA 1"                                              
[3] "alpha 1,4-galactosyltransferase (P blood group)"                     "olfactory receptor family 52 subfamily L member 1 (gene/pseudogene)"
[5] "aladin WD repeat nucleoporin"                                       

GeoTcgaData包的完整教程见：

https://github.com/huerqiang/GeoTcgaData

或者

https://cran.r-project.org/web/packages/GeoTcgaData/readme/README.html