Dear Steffen

I am downloading some snoRNA sequences using biomaRt and it seems that the column names of the final data.frame are swapped.

I am copying my code below.

Thanks for your package

David

> library (biomaRt)
> 
> mart <- useDataset ("hsapiens_gene_ensembl", mart = useMart ("ensembl"))
> 
> mydat <- getBM (c ("ensembl_gene_id", "gene_exon_intron"),
+                 filters = "biotype",
+                 values = "snoRNA",
+                 mart = mart)
> 
> mydat[1:3,]
                                                                                                                         ensembl_gene_id
1                                                                   CAGCCCTAAAATGGAAAAAATTTAAAATTACTTAGACAATGTGATGTCATCAAAGGAACCCTAAGTAA
2                                                      GGGTGGTGATGAGAACCTTGTATTCTTCTGAAGAGAGGTGATGACTTAAAAACCATGCTCAATAGGATTACACTTAGGCCG
3 TCATCAGGTGGGATAATCCTTACCTGTTCCTCGTTTTGGAGGGCAGATAGAACAGGATAATTGGAGTTTGCATGATCCATGATTAATGTCTCTGTGTAATCAGGACTTGCAAACTCTGATTGTTCATATCTGAT
  gene_exon_intron
1  ENSG00000201209
2  ENSG00000200801
3  ENSG00000199713
> 
> sessionInfo ()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.24.0

loaded via a namespace (and not attached):
 [1] IRanges_2.2.1        DBI_0.3.1            parallel_3.2.0      
 [4] RCurl_1.95-4.6       Biobase_2.28.0       AnnotationDbi_1.30.1
 [7] RSQLite_1.0.0        S4Vectors_0.6.0      BiocGenerics_0.14.0 
[10] GenomeInfoDb_1.4.0   stats4_3.2.0         bitops_1.0-6        
[13] XML_3.98-1.1        
> 

Hi David,

That happens with a few query types and the headers are erroneously put on at the BioMart server side, nothing that is fixable from the biomaRt end.  You can overwrite the BioMart headers though with setting bmHeader=FALSE in the getBM query and then things should look fine.  In that case getBM assumes you'll get your columns back in the same order you did the query (which is mostly true) and the headers are put on in R not on the BioMart sever side.

Cheers,

Steffen

Thanks for your quick reply Steffen.

I will just rename the columns as you indicate.

Regard

David

Hi Steffen and David,

I think that in this case, BiomaRt return the wrong header and as a result bmHeader=TRUE should be used instead of FALSE:

> mydat <- getBM (c ("ensembl_gene_id", "gene_exon_intron"),
+                 filters = "biotype",
+                 values = "snoRNA",
+                 mart = mart, bmHeader=TRUE)
> mydat[1:3,]
                                                                                                                        Unspliced (Gene)
1                                                                   CAGCCCTAAAATGGAAAAAATTTAAAATTACTTAGACAATGTGATGTCATCAAAGGAACCCTAAGTAA
2                                                      GGGTGGTGATGAGAACCTTGTATTCTTCTGAAGAGAGGTGATGACTTAAAAACCATGCTCAATAGGATTACACTTAGGCCG
3 TCATCAGGTGGGATAATCCTTACCTGTTCCTCGTTTTGGAGGGCAGATAGAACAGGATAATTGGAGTTTGCATGATCCATGATTAATGTCTCTGTGTAATCAGGACTTGCAAACTCTGATTGTTCATATCTGAT
  Ensembl Gene ID
1 ENSG00000201209
2 ENSG00000200801
3 ENSG00000199713

Kind Regards,

Thomas