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all   attribute   attributes   Attributes   bioma   bm   chromosome   coordinates   dataset   Dataset   Datasets   dmelanogaster   eid2fb   eids   ensembl   entrezgene   Example   filters   flybase   gene   get   how   id   library   list   loci   ma   Mart   mart   Marts   mmusculus   mouse   name   of   position   Rt   start   strand   to   use   using   values  

Clear message

Example of how to get all mouse gene coordinates using biomaRt: 

library(biomaRt)

mouse <- useMart("ensembl", dataset="mmusculus_gene_ensembl")

# check out what's available
ma <- listAttributes(mouse)

loci <- getBM(attribute=c("ensembl_gene_id", "chromosome_name", "start_position", "end_position", "strand"), mart=mouse)


library(biomaRt)

# what marts are available?
listMarts()

bm <- useMart("ensembl")

# what data sets are available?
listDatasets(bm)

bm <- useDataset("dmelanogaster_gene_ensembl", mart=bm)

# for a given list of entrez gene ids, get the flybase ids
eids <- c("35851", "42737", "34411", "35851", "33196", "35851", "43767", "34085", "41565", "41965", "36382", "32772", "41565", "34411", "37618", "43767", "35851", "41565", "40701", "40701", "37618", "33196", "42737", "42737", "42737")

# filter entrezgene
# attributes entrezgene, flybase_gene_id

eid2fb <- getBM(attributes=c("flybase_gene_id"), filters=c("entrezgene"), values=eids, mart=bm)

R/BioMart (last edited 2010-07-28 18:40:55 by ChrisSeidel)