GetBM gives controversial results

I want to get chromosome location of SMARCA1 gene.

library("biomaRt")
human = useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl",host="grch37.ensembl.org", path="/biomart/martservice")
getBM(attributes = c("hgnc_symbol","chromosome_name", "start_position", 
                     "end_position","strand"),
     filters = "hgnc_symbol", values = "SMARCA1", mart = human)

I have a table after running this code:

hgnc_symbol chromosome_name start_position end_position strand
1     SMARCA1               X      128580480    128657477     -1

Then, I search for this very gene in the region it should be located:

getBM(attributes = c("hgnc_symbol","chromosome_name", "start_position", "end_position","strand", "transcript_length","ensembl_transcript_id"),
filters = c("chromosome_name","start","end"),
values = list("chrX", 128580480, 128657477),mart = human)

and get nothing:

[1] hgnc_symbol           chromosome_name       start_position        end_position          strand                transcript_length     ensembl_transcript_id
<0 rows> (or 0-length row.names)

How is this possible?

gene bioconductor biomart r

• 1,816 views • link

written 7.9 years ago by lizaveta •

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

• 1 views • link

written 7.9 years ago by Kevin Blighe

1 answer

set chromosome_name to X not chrX in your getBM

• 1 views • link

written 7.9 years ago by russhh

More posts like this

Getting chromosome of unusual chromosome names e.g. 'CHR_HSCHR8_8_CTG1'
written 3.3 years ago by 4galaxy77

I made a biomaRt query: ``` library(biomaRt) mart = useMart('ensembl', dataset = 'hsapiens_gene_ensembl') genes = getBM(attributes = c("chromosome_name","start_position", "hgnc_symbol", "uniprot_gn_symbol", "uniprot_gn_id"), mart = mart, values …
biomaRt: Timeout on getBM().
written 5.1 years ago by lincaijin1994 •

Hi. I want to get the exon annotation of a list of chromosome interval (hg19). Here is the code: getBM_value <- list( chromosome_name = bed_df$chromosome_name, …
gene ensemble ID- no symbol
written 5.4 years ago by Rob •

Hello friends, I used this code to convert ensemble gene ID to gene symbol: df <- read.csv("gene_Ens_ID.csv") library('biomaRt') mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl")) attributeNames <- c('ensembl_gene_id','external_gene_name','description','gene_biotype', …
annotation - biomaRt - Error in UseMethod
written 5.7 years ago by ferreira.cristina •

Hi, I try run the getBM from biomaRt but a error was returned. ensembl=useMart("ENSEMBL_MART_ENSEMBL") ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) list <- c("DUOX2", "DIRAS3") x <- getBM(attributes = …
annotation - biomaRt - getBM - multiple entrez ID
written 7.6 years ago by Learner

Hi I am trying to follow what is said in here , however, without any success https://support.bioconductor.org/p/52407/ when I do it as described here, I …
Map ensembl gene id form hg38 in hg19
written 10.2 years ago by Tanvir Ahamed

I want to map all ensembl gene id form hg38 in hg19. Any help will be appreciated ? Thanks !! # Example : Loading library …
biomaRt LPR region to position giving different results than I expect (using R)
written 10.8 years ago by Niek De Klein

I am trying to map some ensembl gene IDs and LRG regions to position on the genome. I got the gene IDs and LRG regions …
biomart gene coordinates do not correspond to genome browser
written 11.4 years ago by tonja.r

I was annotating my dataset with biomart with filtering by chromosomal region and was surprised by the genes I got, so I took a closer …
BiomaRT, retrieve exon positions but filter to chrosomal region
written 11.4 years ago by tonja.r

I am using biomart to retrieve gene/transcripts/exon information and I need exon start and end positions BUT before I need to filter according to the …
Empty gene names from ensembl query using biomart
written 11.7 years ago by kindlychung •

Here is the code: ``` require(biomaRt) ensembl = useMart("ensembl", ,dataset="hsapiens_gene_ensembl") # filters = listFilters(ensembl) # filters[1:5, ] # attributes = listAttributes(ensembl) # ensembl_attr = cbind(attributes$name, …