[biomaRt] Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed

正文

Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed

就如报错所说， 来源于多个attribute pages 的attributes 被设置.

举个例子：

我有一个 exon ,其id为 ENSE00001706048， 查询其对应的基因id：

## 设置数据库和数据集
human <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl", mirror = "asia")

results <- getBM(
    attributes= c("ensembl_gene_id", "external_gene_name", "ensembl_exon_id"),
    filters=c("ensembl_exon_id"),
    values="ENSE00001706048", mart=human)

> results
  ensembl_gene_id external_gene_name ensembl_exon_id
1 ENSG00000188554               NBR1 ENSE00001706048

当我们还想，知道exon 的起始，和终止位置时, 加上两个attributes:

results <- getBM(
    attributes= c("ensembl_gene_id", "external_gene_name","ensembl_exon_id", 
                  "exon_chrom_start", "exon_chrom_end"),
    filters=c("ensembl_exon_id"),
    values="ENSE00001706048", mart=human)

也能正常得出我们想要的结果：

> results
  ensembl_gene_id external_gene_name ensembl_exon_id exon_chrom_start exon_chrom_end
1 ENSG00000188554               NBR1 ENSE00001706048         43200167       43200608

进一步，若还想知道gene 对应的GO term有哪些, 尝试添加go_id, 这个attribute。

results <- getBM(
    attributes= c("ensembl_gene_id", "external_gene_name", "ensembl_exon_id", 
                  "exon_chrom_start", "exon_chrom_end", "go_id"),
    filters=c("ensembl_exon_id"),
    values="ENSE00001706048", mart=human)

很遗憾，它报错了

Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery,  : 
  Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed

我们查看下我们设置的attributes,

e_attrs <- c("ensembl_gene_id", "external_gene_name", "ensembl_exon_id",  "exon_chrom_start", "exon_chrom_end", "go_id")

listAttributes(human)[listAttributes(human)$name %in% e_attrs, ]

"ensembl_gene_id", "external_gene_name","ensembl_exon_id", "exon_chrom_start", "exon_chrom_end" 都属于structure 这个page, 而feature_page 这个page下，有"go_id", 但没有"exon_chrom_start", "exon_chrom_end"。

所以就如报错所说， 来源于多个attribute pages 的attributes 被设置. "exon_chrom_start", "exon_chrom_end" 和"go_id" 混在一起报错了。

解决方法

分开查询，然后合并了。

results1 <- getBM(
    attributes= c("ensembl_gene_id", "external_gene_name", "ensembl_exon_id", 
                  "exon_chrom_start", "exon_chrom_end"),
    filters=c("ensembl_exon_id"),
    values="ENSE00001706048", mart=human)

results2 <- getBM(
  attributes= c("ensembl_gene_id", "external_gene_name", "ensembl_exon_id", "go_id"),
  filters=c("ensembl_exon_id"),
  values="ENSE00001706048", mart=human)

merge(results1, results2)

> merge(results1, results2)
   ensembl_gene_id external_gene_name ensembl_exon_id exon_chrom_start exon_chrom_end      go_id
1  ENSG00000188554               NBR1 ENSE00001706048         43200167       43200608 GO:0008270
2  ENSG00000188554               NBR1 ENSE00001706048         43200167       43200608 GO:0005515
3  ENSG00000188554               NBR1 ENSE00001706048         43200167       43200608 GO:0043130
4  ENSG00000188554               NBR1 ENSE00001706048         43200167       43200608 GO:0000407
5  ENSG00000188554               NBR1 ENSE00001706048         43200167       43200608 GO:0016236
...........
23 ENSG00000188554               NBR1 ENSE00001706048         43200167       43200608 GO:0051019
24 ENSG00000188554               NBR1 ENSE00001706048         43200167       43200608 GO:0032872
25 ENSG00000188554               NBR1 ENSE00001706048         43200167       43200608 GO:0005758

其他

listAttributes 函数可以列出，可查询返回的attributes ,listFilters可以列出可以用于筛选的attributes

> ensembl <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl", mirror = "asia")
> listAttributes(ensembl)
                           name                  description         page
1               ensembl_gene_id               Gene stable ID feature_page
2       ensembl_gene_id_version       Gene stable ID version feature_page
3         ensembl_transcript_id         Transcript stable ID feature_page
4 ensembl_transcript_id_version Transcript stable ID version feature_page
5            ensembl_peptide_id            Protein stable ID feature_page
6    ensembl_peptide_id_version    Protein stable ID version feature_page
..........
..........


> listFilters(ensembl)
                name                            description
1    chromosome_name               Chromosome/scaffold name
2              start                                  Start
3                end                                    End
4             strand                                 Strand
5 chromosomal_region e.g. 1:100:10000:-1, 1:100000:200000:1
......
.....

以及biomaRt， 是个好东西，就是经常提醒我请求尝试超时...

Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [asia.ensembl.org:443] Connection timed out after 10001 milliseconds

参考

https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/accessing_ensembl.html
https://support.bioconductor.org/p/33414/