org.Hs.eg.db使用--持续修改-CSDN博客

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org.Hs.eg.db使用–持续修改

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library(org.Hs.eg.db)

1 基本信息查询

1.1 display the columns

columns(org.Hs.eg.db)
[1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS" "ENTREZID"     "ENZYME"       "EVIDENCE"    
[9] "EVIDENCEALL"  "GENENAME"     "GENETYPE"     "GO"           "GOALL"        "IPI"          "MAP"          "OMIM"        
[17] "ONTOLOGY"     "ONTOLOGYALL"  "PATH"         "PFAM"         "PMID"         "PROSITE"      "REFSEQ"       "SYMBOL"      
[25] "UCSCKG"       "UNIPROT"

1.2 get the 1st 6 possible keys

keys <- head( keys(org.Hs.eg.db) )

2 信息提取

2.1 提取想要的列,如与SYMBOL的对应关系

keys <- keys(org.Hs.eg.db) 
select(org.Hs.eg.db, keys=keys, columns = c("ENSEMBL","SYMBOL")) %>% head()
ENTREZID         ENSEMBL SYMBOL
1        1 ENSG00000121410   A1BG
2        2 ENSG00000175899    A2M
3        3 ENSG00000256069  A2MP1
4        9 ENSG00000171428   NAT1
5       10 ENSG00000156006   NAT2
6       11            <NA>   NATP

library(biomaRt)
listMarts()
listAttributes(mart)
mart<-useMart("ENSEMBL_MART_ENSEMBL","hsapiens_gene_ensembl")
report_gene<- getBM(attributes=c('ensembl_gene_id','hgnc_symbol',"chromosome_name",
                                "start_position","end_position", "band"), 
                   filters= 'external_gene_name', values= report_gene, mart = mart)