getHomolog              package:biomaRt              R Documentation

_G_e_t _h_o_m_o_l_o_g_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function retrieves homologs of genes from one species in
     another species

_U_s_a_g_e:

     getHomolog(id, from.type, to.type, from.mart, to.mart)

_A_r_g_u_m_e_n_t_s:

      id: gene identifier

from.type: type of identifier of the input. Possible values depend on
          the selected species and can be obtained by the listFilters
          function and using the from.mart.  Examples for hsapiens are:
          entrezgene, hgnc (for hugo gene symbol), ensembl_gene_id,
          unigene, agilentprobe, affy_hg_u133_plus_2,  refseq_dna, etc.

 to.type: type of identifier that needs to be retrieved from as homolog
          id. Possible values depend on the selected species and can be
          obtained by the listAttributes function and using the
          to.mart.  Examples for hsapiens are entrezgene, hgnc (for
          hugo gene symbol), ensembl_gene_id, unigene, agilentprobe,
          affy_hg_u133_plus_2,  refseq_dna, etc. 

from.mart: Mart object using dataset from species of which the query id
          is from.

 to.mart: Mart object using dataset from species you want to find the
          homologs off.

_A_u_t_h_o_r(_s):

     Steffen Durinck, Sean Davis

_E_x_a_m_p_l_e_s:

     if(interactive()){
     from.mart <- useMart("ensembl","hsapiens_gene_ensembl")
     to.mart <- useMart("ensembl","mmusculus_gene_ensembl")

     #HUGO to Entrez Gene

     homolog = getHomolog(id = 1:20, from.mart = from.mart, to.mart = to.mart, from.type = 'entrezgene', to.type = 'refseq_dna')
     show(homolog)

     #ensembl to ensembl

     homolog = getHomolog( id = "ENSG00000072778", from.mart = from.mart, from.type = "ensembl_gene_id", to.type="ensembl_gene_id",to.mart=to.mart)
     show(homolog)

     #Affy to Affy

     homolog = getHomolog( id = "1939_at", to.type = "affy_mouse430_2", from.type = "affy_hg_u95av2", from.mart = from.mart, to.mart=to.mart )
     show(homolog)

     #Ensembl to Affy

     homolog = getHomolog( id = "ENSG00000072778", to.type = "affy_mouse430_2", from.type = "ensembl_gene_id", from.mart = from.mart, to.mart = to.mart )
     show(homolog)

     }

