library(biomaRt)#需要注釋的是hg19版本的21個乳腺癌相關(guān)基因，基因名稱如下gene_list <->'CCNB1', 'MKI67', 'MYBL2', 'AURKA', 'BIRC5', 'CTSV', 'MMP11', 'ACTB', 'GAPDH', 'GUSB', 'RPLP0', 'TFRC', 'BCL2', 'SCUBE2', 'ESR1', 'PGR', 'GRB7', 'ERBB2', 'BAG1', 'CD68', 'GSTM1')length(gene_list)
#直接使用默認(rèn)的數(shù)據(jù)庫, 'www.ensembl.org'是默認(rèn)鏈接mart <- usemart(biomart="">'ENSEMBL_MART_ENSEMBL', dataset = 'hsapiens_gene_ensembl')database <->1]=='hsapiens_gene_ensembl',] #可以看到使用的搜hg38的基因組
gene_info <- getbm(attributes="">'ensembl_gene_id', 'external_gene_name', 'description'), filters = 'external_gene_name', values = gene_list, mart = mart)dim(gene_info)#由于基因組版本不匹配，多注釋出一個基因
#MMP11在hg38基因組上對應(yīng)兩個gene id
#鏈接改為'grch37.ensembl.org'mart <- usemart(host="">'grch37.ensembl.org', biomart = 'ENSEMBL_MART_ENSEMBL', dataset = 'hsapiens_gene_ensembl')database <->1]=='hsapiens_gene_ensembl',]#可以看到使用的搜hg38的基因組
gene_info <- getbm(attributes="">'ensembl_gene_id', 'external_gene_name', 'description'), filters = 'external_gene_name', values = gene_list, mart = mart)dim(gene_info)
#重新注釋結(jié)果正常