getBM error in R while retrieving IDs and missing GC values

Hi All

I am trying to retrieve attributes from BioMart in R and run into the following issue:

> ensAtt = getBM(attributes = "chromosome_name", "start_position", "end_position", values = eList, filters = "ensembl_gene_id", mart=ensembl, verbose = verbose)

The error message is: Error in filters[1] != "" && checkFilters : invalid 'y' type in 'x && y'

All the parameters are pre-defined and there are no missing values in my values=eList. Since the values=eList that I am using is a long list (>15000), so I have also tried breaking the it into smaller chunks values = eList[1:1000] but to no avail.

Also if I try to retrieve another attribute (GC content) using:

gc = getBM(attributes = "percentage_gene_gc_content", values = eList, filters = "ensembl_gene_id", mart=ensembl)

I don"t have any problems with the command although the returned data matrix has only 2608 values (instead of the expected >15000). Is it possible that ENSEMBL has no data for such IDs? Or I am missing something here.

Thank you for all your expected help.

Best M

r software error

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written 9.2 years ago by manu.tiwari •

Should it be attributes = c("chromosome_name", "start_position", ...)

• 0 views • link

written 9.2 years ago by russhh

Thanks for the hint. It works now.

• 0 views • link

written 9.2 years ago by manu.tiwari •

0 answers

No answers yet.

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