geneRegionBiomart        package:GenomeGraphs        R Documentation

_C_o_n_s_t_r_u_c_t _a_n _A_n_n_o_t_a_t_i_o_n_T_r_a_c_k _o_b_j_e_c_t _f_r_o_m _b_i_o_m_a_R_t.

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

     This function constructs an AnnotationTrack object from Biomart.
     It is a convenience function.

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

     geneRegionBiomart(chr, start, end, strand, biomart, dp = NULL, chrFunction = function(x) x, strandFunction = function(x) x)

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

     chr: 'chr' An integer

   start: 'start' The start location 

     end: 'end' The end location 

  strand: 'strand' An integer -1, 0, 1

 biomart: 'biomart' A mart

      dp: 'dp' DisplayPars object

chrFunction: 'chrFunction' A function which takes 'chr' and converts it
          into the correct representation for biomaRt. For instance
          yeast likes to have chromosomes as roman numerals so you can
          use as.roman here.

strandFunction: 'strandFunction' Analagous to chrFunction, but for
          strand. The internal representation of strand is -1,0,1
          whereas biomaRt has different species dependent
          representations.

_V_a_l_u_e:

     An AnnotationTrack object.

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

     James Bullard

