getFeature              package:biomaRt              R Documentation

_R_e_t_r_i_e_v_e_s _i_d_e_n_t_i_f_i_e_r_s _s_t_a_r_t_i_n_g _f_r_o_m _a _g_e_n_e _s_y_m_b_o_l, _c_h_r_o_m_o_s_o_m_a_l _p_o_s_i_t_i_o_n _o_r _G_O _i_d_e_n_t_i_f_i_e_r

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

     This function function retrieves identifiers representing a
     certain gene given a gene symbol, chromosomal positions or GO
     identifier

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

     getFeature( symbol, OMIMID, GOID, chromosome, start, end, type, mart)

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

  symbol: gene symbol

  OMIMID: OMIM identifier

    GOID: GO identifier

chromosome: chromosome, can be used without start and end positions

   start: start on chromosome

     end: end on chromosome

    type: type of identifier that needs to be retrieved, possible
          values can be obtained by the listFilters function.  Examples
          are  entrezgene, hgnc_symbol (for hugo gene symbol),
          ensembl_gene_id, unigene, agilentprobe, refseq_dna,
          affy_hg_u133_plus_2,  etc.

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

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

     Steffen Durinck

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

     if(interactive()){
     mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl")

     #example using affy id from Ensembl

     feat = getFeature( symbol = "TP53",type  = "affy_hg_u95av2", mart = mart)
     show(feat)
     }

