makeGeneRegion         package:GenomeGraphs         R Documentation

_C_r_e_a_t_e_s _a_n _o_b_j_e_c_t _o_f _c_l_a_s_s _G_e_n_e _c_o_n_t_a_i_n_i_n_g _t_h_e _i_n_t_r_o_n-_e_x_o_n _s_t_r_u_c_t_u_r_e_s _o_f _g_e_n_e_s

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

     Creates an object of class Gene containing the intron-exon
     structures of genes. Given a start and end position, strand and
     chromosome, all the intron-exon strcutures of all genes laying in
     this region will be retrieved.

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

     makeGeneRegion(start, end, chromosome, strand, biomart, dp = NULL)

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

   start: Start position on chromosome

     end: End position on chromosome

chromosome: Chromosome name

  strand: Strand either + or -

 biomart: Mart object, created by the useMart function of biomaRt

      dp: Object of class DisplayPars, determines the display of
          features on the plot

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

     An object of class Gene

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

     Steffen Durinck and Jim Bullard

_R_e_f_e_r_e_n_c_e_s:

     ~put references to the literature/web site here ~

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

     'gdPlot'

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

     ##---- Should be DIRECTLY executable !! ----
     ##-- ==>  Define data, use random,
     ##--    or do  help(data=index)  for the standard data sets.

     ## The function is currently defined as
     function (start, end, chromosome, strand, biomart, dp = NULL) 
     {
         if (missing(start)) 
             stop("Need to specify a start for creating a GeneRegion")
         pt <- getClass("GeneRegion")@prototype
         if (is.null(dp)) 
             dp <- pt@dp
         if (is.numeric(chromosome)) 
             chromosome = as.character(chromosome)
         new("GeneRegion", start = start, end = end, chromosome = chromosome, 
             strand = strand, biomart = biomart, dp = dp)
       }

