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.  For genomic sequences the strand that is returned
     is the 5' t0 3' strand. Note that using this function with MySQL
     is limited to genomic sequences.

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

     getSequence( chromosome, start, end, id, type, seqType, mart)

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

chromosome: Chromosome name

   start: start position of sequence on chromosome

     end: end position of sequence on chromosome

      id: An identifier or vector of identifiers.

    type: The type of identifier used.  Supported types are hugo,
          ensembl, embl, entrezgene, refseq, ensemblTrans and unigene.

 seqType: Type of sequence that you want to retrieve.  Allowed seqTypes
          are: cdna, peptide, 3utr, 5utr, genomic

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

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

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

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

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

     seq = getSequence(id="BRCA1", type="hugo", seqType="peptide", mart = mart)
     show(seq)

     martDisconnect(mart = mart)
     }

