r - 使用 Biomart hsapiens_gene_ensembl 数据集时出现错误消息。有谁知道如何解决吗？

Question

这是我用来尝试连接到 hsapiens 数据集的代码:

 > mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL",
 +                          dataset = "hsapiens_gene_ensembl",
 +                          host = "www.ensembl.org")

这是控制台中显示的错误消息:

 Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : 
 The given dataset:  
 hsapiens_gene_ensembl , is not valid.  
 Correct dataset  names can be obtained with the listDatasets function.

我很困惑为什么会收到此错误，因为它说该数据集是无效的数据集，但我检查过，它确实有效。

Answer 1

您需要使用host = "http://www.ensembl.org" 参数:

mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                         dataset = "hsapiens_gene_ensembl",
                         host = "http://www.ensembl.org")

str(mart)
#     Formal class 'Mart' [package "biomaRt"] with 8 slots
#   ..@ biomart   : chr "ENSEMBL_MART_ENSEMBL"
#   ..@ host      : chr "http://www.ensembl.org:80/biomart/martservice"
#   ..@ vschema   : chr "default"
#   ..@ version   : chr(0) 
#   ..@ dataset   : chr "hsapiens_gene_ensembl"
# ...