getSequence             package:biomaRt             R Documentation

_R_e_t_r_i_e_v_e_s _s_e_q_u_e_n_c_e_s

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

     This function retrieves sequences given the chomosome, start and
     end position

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

     getSequence( species, chromosome, start, end, martTable, mart)

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

 species: Species information.  A list of possible values for this
          argument can be obtained by the function getSpecies.

chromosome: Chromosome name

   start: start position of sequence on chromosome

     end: end position of sequence on chromosome

martTable: alternatively a martTable can be used containing all
          information

    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, <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(biomarts = c("ensembl","sequence"))

     seq = getSequence(species="ggallus", chromosome = 1, start = 400, end = 500, mart = mart)
     show(seq)

     martDisconnect(mart = mart)
     }

