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.array, to.array, from.species, to.species, mart, output = "martTable")

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

      id: gene identifier

from.type: type of identifier, value should be either entrezgene, embl
          or refseq

 to.type: type of identifier, value should be either entrezgene, embl
          or refseq

from.array: Affy array from which the input identifiers come.  Note if
          this has a value then you don't have to specify from.type and
          from.species.

to.array: Affy array to which you want to map.  Note if this has a
          value then you don't have to specify to.type and to.species.

from.species: species of which the id is from.  Accepted values for
          species can be retrieved with the function getSpecies()

to.species: species in which you want to find the homologs.  Accepted
          values for species can be retrieved with the function
          getSpecies()

    mart: object of class Mart, containing connections to the BioMart
          databases.  You can creat such an object using the function
          martConnect.

  output: desired output type, object of class martTable

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

     Sean Davis, Steffen Durinck, <URL:
     http://www.esat.kuleuven.ac.be/~sdurinck>

_S_e_e _A_l_s_o:

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

     if(interactive()){
     mart <- martConnect()

     #HUGO to Entrez Gene

     homolog = getHomolog(id = 1:20, from.species = 'hsapiens', to.species = 'mmusculus', from.type = 'entrezgene', to.type = 'refseq', mart = mart)
     show(homolog)

     #ensembl to ensembl

     homolog = getHomolog( id = "ENSG00000072778", from.species = "hsapiens", from.type = "ensembl", to.type="ensembl",to.species="mmusculus", mart = mart )
     show(homolog)

     #Affy to Affy

     homolog = getHomolog( id = "1424184_at", to.array = "hg_u95av2", from.array = "mouse430a_2", mart = mart )
     show(homolog)

     #Affy to ensembl

     homolog = getHomolog( id = "1424184_at", to.species = "hsapiens", to.type = "ensembl", from.array = "mouse430a_2", mart = mart )
     show(homolog)

     martDisconnect(mart = mart)
     }

