Loading... # 安装 ```R if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("biomaRt") ``` # 使用 # 示例 ## 将mrna转换为ensembl_gene_id或entrezgene_id ```R get_Ensembl_by_Refseq <- function(refseq_mrna){ ensembl <- biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl") tt <- biomaRt::getBM(attributes = c('ensembl_gene_id', 'refseq_mrna'), filters = 'refseq_mrna', values = refseq_mrna, mart = ensembl) if (nrow(tt) == 0){ return(NA) } else{ return(tt) } } get_Ensembl_by_Refseq(c("NM_001002811","NM_001198834","NM_014644","NM_001198832","NM_001002812","NM_001278267","NM_001277444")) -> ee r$> ee ensembl_gene_id refseq_mrna 1 ENSG00000178104 NM_001002811 2 ENSG00000178104 NM_001002812 3 ENSG00000178104 NM_001198832 4 ENSG00000178104 NM_001198834 5 ENSG00000269713 NM_001277444 6 ENSG00000162825 NM_001278267 7 ENSG00000178104 NM_014644 ``` ## 从ncbi gene id获取基因在染色体上的位置 ```R get_BP_by_ID <- function(gene_id){ ensembl <- biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "grch37.ensembl.org") # gene_id <- "96626" # 替换为您感兴趣的基因ID attributes <- c("entrezgene_id", "start_position", "end_position", "chromosome_name") filters <- "entrezgene_id" values <- gene_id gene_info <- biomaRt::getBM(attributes = attributes, filters = filters, values = values, mart = ensembl) return(gene_info) } r$> get_BP_by_ID(c(96626,1)) entrezgene_id start_position end_position chromosome_name 1 1 58856544 58864865 19 2 96626 110656005 110677180 2 3 96626 111222628 111230511 2 ``` ## 将ensembl_id转换为NCBI Gene Symbol和entrezgene_id ```R convert_to_ncbi_gene_symbol <- function(ensembl_ids) { ensembl <- biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl") genes <- biomaRt::getBM(attributes = c('ensembl_gene_id', 'external_gene_name'), filters = 'ensembl_gene_id', values = ensembl_ids, mart = ensembl) return(genes) } ``` 最后修改：2024 年 02 月 03 日 © 允许规范转载 赞 如果觉得我的文章对你有用，请随意赞赏