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Example snippet showing how to query BioMart from R, to find mRNA Refseq Ids associated with mouse gene symbols.
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# This snippet queries BioMart to find mRNA Refseq Ids associated with mouse gene symbols. | |
# Load biomaRt. | |
library(biomaRt) | |
# Get vector of gene symbols from a table loaded in R. | |
genes <- mytable$Gene | |
# Choose BioMart database and dataset. | |
mart <- useMart("ensembl", dataset="mmusculus_gene_ensembl") | |
# Specify filter used to read input values. | |
# A list of possible filters can be retrieved using listFilters. | |
filters=c("mgi_symbol") | |
# Specify attributes to be returned. | |
# A list of possible attributes can be retrieved using listAttributes. | |
attributes <- c("chromosome_name", "start_position", "end_position", "mgi_symbol", "refseq_mrna") | |
# Retrieve attributes for submitted genes. | |
mynewtable <- getBM(attributes=attributes, filters=filters, values=genes, mart=mart, uniqueRows=T) |
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