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@davebridges
Last active August 29, 2015 14:11

Revisions

  1. davebridges revised this gist Dec 17, 2014. 1 changed file with 1 addition and 1 deletion.
    2 changes: 1 addition & 1 deletion sample mapping code
    Original file line number Diff line number Diff line change
    @@ -8,7 +8,7 @@ dataset <- read.csv('Hits_PvsM_HighinMimic_filt.csv')
    #you have several different ensembl results
    unique(substr(dataset$Gene, 1,7))

    #get a mapping file to convert stickleback to Danio rerio
    #get a mapping file to get externam gene names from stickleback
    stickleback_table <- getBM(attributes=c('ensembl_gene_id','external_gene_name','entrezgene'),
    filters='ensembl_gene_id',
    values=dataset$Gene,
  2. davebridges created this gist Dec 17, 2014.
    20 changes: 20 additions & 0 deletions sample mapping code
    Original file line number Diff line number Diff line change
    @@ -0,0 +1,20 @@
    library(biomaRt)
    ensembl=useMart("ensembl")
    #show possible datasets
    listDatasets(ensembl)

    #your results are listed here
    dataset <- read.csv('Hits_PvsM_HighinMimic_filt.csv')
    #you have several different ensembl results
    unique(substr(dataset$Gene, 1,7))

    #get a mapping file to convert stickleback to Danio rerio
    stickleback_table <- getBM(attributes=c('ensembl_gene_id','external_gene_name','entrezgene'),
    filters='ensembl_gene_id',
    values=dataset$Gene,
    mart=useDataset("gaculeatus_gene_ensembl",mart=ensembl))
    #repeat this with other species in your results set by changing the species in the use dataset.
    #To find the abbreviation for that species use listDatasets(ensembl)
    mapped_table <- rbind(stickleback_table) #add other tables

    write.csv(mapped_table, file="Mapped Genes.csv")