biomaRt: getting start and end locations of gene on chromosome
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.1 years ago
Hi, Given a set of entrez IDs, I wanted to know their start and end locations on the chromosome. I am using biomaRt, but get the following error: ------------------------------------------- > entrezID = "7471" > getBM(attributes = c('hgnc_symbol','chromosome_name','start_position', + 'end_position'),mart = ensembl, filters = 'with_entrezgene', + values = entrezID) Error in getBM(attributes = c("hgnc_symbol", "chromosome_name", "start_position", : biomaRt error: with_entrezgene is a boolean filter and needs a corresponding logical value of TRUE or FALSE to indicate if the query should retrieve all data that fulfill the boolean or alternatively that all data that not fulfill the requirement should be retrieved. ------------------------------------------- I read the documentation and it said that this particular filter needs a boolean value (error statement says the same), but it didn't say how I was actually to set it. How do I go about doing this? thanks! [[alternative HTML version deleted]]
GO biomaRt GO biomaRt • 2.8k views
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@james-w-macdonald-5106
Last seen 2 days ago
United States
Hi Tim, I would replace "with_entrezgene" with "entrezgene": >getBM(c('hgnc_symbol','chromosome_name','start_position','end_positi on'), "entrezgene",entrezID, mart) hgnc_symbol chromosome_name start_position end_position 1 WNT1 12 47658503 47662746 I would also add entrezID to the attributes - it helps to know what things you didn't get, as well as things that map to the same ID more than once. Best, Jim Tim Smith wrote: > Hi, > > Given a set of entrez IDs, I wanted to know their start and end locations on the chromosome. I am using biomaRt, but get the following error: > > ------------------------------------------- > >> entrezID = "7471" >> getBM(attributes = c('hgnc_symbol','chromosome_name','start_position', > + 'end_position'),mart = ensembl, filters = 'with_entrezgene', > + values = entrezID) > > Error in getBM(attributes = c("hgnc_symbol", "chromosome_name", "start_position", : > biomaRt error: with_entrezgene is a boolean filter and needs a corresponding logical value of TRUE or FALSE to indicate if the query should retrieve all data that fulfill the boolean or alternatively that all data that not fulfill the requirement should be retrieved. > ------------------------------------------- > > I read the documentation and it said that this particular filter needs a boolean value (error statement says the same), but it didn't say how I was actually to set it. How do I go about doing this? > > thanks! > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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Hi James,

I am having similar problem with biomRt when I want to retrieve annotation for prob IDs from Affymetrix HTA2.0.

My code is as follow;


ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
filters <- listFilters(ensembl)
attributes <- listAttributes(ensembl)

genes <- getBM(attributes = c("affy_hta_2_0", "ensembl_gene_id","ensembl_transcript_id","external_gene_name","entrezgene", "gene_biotype","transcript_biotype", "go_id","strand","chromosome_name","status","transcript_status","transcript_length","description"),
               filters = "with_affy_hta_2_0",
               values = '2824546_st',
               mart = ensembl)

I also tried to set the filter as "affy_hta_2_0" but failed to retrieve the annotation.

what the problem can possibly be ?

thanks.

Hossein

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