BiomaRt: archive version of ensembl not working
2
1
Entering edit mode
5.8 years ago
salamandra ▴ 550

Hi,

I want to access an archived version of biomart and select the human dataset.

mart=useMart("ensembl_mart_92",host="http://apr2018.archive.ensembl.org")

works but if I do:

mart=useMart("ensembl_mart_92",host="http://apr2018.archive.ensembl.org", dataset = "hsapiens_gene_ensembl")

it gives error:

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

If I look into listDatasets() as suggested I get:

mart=useMart("ensembl_mart_92",host="http://apr2018.archive.ensembl.org")
listDatasets(mart)
[1] dataset     description version    
<0 rows> (or 0-length row.names)

Also tried other suggestions online that didn't work:

listMarts(archive = TRUE)

Error in listMarts(archive = TRUE) : 
The archive = TRUE argument is now defunct.
Use listEnsemblArchives() to find the URL to directly query an Ensembl archive.


listEnsemblArchives()
             name     date                                url version current_release
1  Ensembl GRCh37 Feb 2014          http://grch37.ensembl.org  GRCh37                
2      Ensembl 94 Oct 2018 http://oct2018.archive.ensembl.org      94               *
3      Ensembl 93 Jul 2018 http://jul2018.archive.ensembl.org      93                
4      Ensembl 92 Apr 2018 http://apr2018.archive.ensembl.org      92                
5      Ensembl 91 Dec 2017 http://dec2017.archive.ensembl.org      91                
6      Ensembl 90 Aug 2017 http://aug2017.archive.ensembl.org      90                
7      Ensembl 89 May 2017 http://may2017.archive.ensembl.org      89                
8      Ensembl 88 Mar 2017 http://mar2017.archive.ensembl.org      88                
9      Ensembl 87 Dec 2016 http://dec2016.archive.ensembl.org      87                
10     Ensembl 86 Oct 2016 http://oct2016.archive.ensembl.org      86                
11     Ensembl 85 Jul 2016 http://jul2016.archive.ensembl.org      85                
12     Ensembl 84 Mar 2016 http://mar2016.archive.ensembl.org      84                
13     Ensembl 83 Dec 2015 http://dec2015.archive.ensembl.org      83                
14     Ensembl 82 Sep 2015 http://sep2015.archive.ensembl.org      82                
15     Ensembl 81 Jul 2015 http://jul2015.archive.ensembl.org      81                
16     Ensembl 80 May 2015 http://may2015.archive.ensembl.org      80                
17     Ensembl 79 Mar 2015 http://mar2015.archive.ensembl.org      79                
18     Ensembl 78 Dec 2014 http://dec2014.archive.ensembl.org      78                
19     Ensembl 77 Oct 2014 http://oct2014.archive.ensembl.org      77                
20     Ensembl 76 Aug 2014 http://aug2014.archive.ensembl.org      76                
21     Ensembl 75 Feb 2014 http://feb2014.archive.ensembl.org      75                
22     Ensembl 74 Dec 2013 http://dec2013.archive.ensembl.org      74                
23     Ensembl 67 May 2012 http://may2012.archive.ensembl.org      67                
24     Ensembl 54 May 2009 http://may2009.archive.ensembl.org      54   

mart=useMart("ensembl_mart_92", dataset="hsapiens_gene_ensembl", archive=T)

rror in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  : 
The archive = TRUE argument is now defunct.


mart=useMart("ensembl_mart_92", dataset="hsapiens_gene_ensembl")

Error in useMart("ensembl_mart_92", dataset = "hsapiens_gene_ensembl") : 
Incorrect BioMart name, use the listMarts function to see which BioMart databases are available

listMarts()
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 94
2   ENSEMBL_MART_MOUSE      Mouse strains 94
3     ENSEMBL_MART_SNP  Ensembl Variation 94
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 94

I'm walking in circles here...Suggestions??

biomart r • 6.6k views
ADD COMMENT
0
Entering edit mode

Tagging: Emily_Ensembl

ADD REPLY
8
Entering edit mode
5.8 years ago
Emily 24k

Try:

> mart=useMart("ensembl",host="http://apr2018.archive.ensembl.org", dataset = "hsapiens_gene_ensembl")
ADD COMMENT
0
Entering edit mode

thank you very much!

ADD REPLY
5
Entering edit mode
5.8 years ago
Mike Smith ★ 2.1k

Emily's answer is correct, but you can also use the following which may be easier to remember than specifying the archive URL directly:

mart <- useEnsembl(biomart = "ensembl", 
                   dataset = "hsapiens_gene_ensembl", 
                   version = "92")
ADD COMMENT

Login before adding your answer.

Traffic: 1445 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6