GeneRegion-class        package:GenomeGraphs        R Documentation

_C_l_a_s_s "_G_e_n_e_R_e_g_i_o_n", _r_e_p_r_e_s_e_n_t_i_n_g _g_e_n_e _s_t_r_u_c_t_u_r_e_s _i_n _a _d_e_f_i_n_e_d _g_e_n_o_m_i_c _r_e_g_i_o_n

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

     Given a start and end position and a chromosome name, all gene
     structures in this region will be retrieved from Ensembl upon
     creation of the object.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("GeneRegion",
     ...)'.

_S_l_o_t_s:


     '_s_t_a_r_t': Object of class '"numeric"', start position

     '_e_n_d': Object of class '"numeric"', end position 

     '_c_h_r_o_m_o_s_o_m_e': Object of class '"character"', chromosome name 

     '_s_t_r_a_n_d': Object of class '"character"', represents the strand
          from which the gene structures should be retrieved.  Value is
          either + or -

     '_s_i_z_e': Object of class '"numeric"', represents the size of the
          GeneRegion in the final plot 

     '_c_o_l_o_r': Object of class '"character"', represents the color to be
          used to plot the exons 

     '_b_i_o_m_a_r_t': Object of class '"Mart"', containing the link to the
          Ensembl database.  This should be created by the useMart
          function from the biomaRt package

     '_e_n_s': Object of class '"data.frame"', output of the biomaRt
          query, should not be used by users

_M_e_t_h_o_d_s:


     _d_r_a_w_G_D 'signature(.Object = "GeneRegion")': ...     

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "GeneRegion")': ... 

     _s_h_o_w 'signature(object = "GeneRegion")': ... 

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

     Steffen Durinck

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

     http://www.stat.berkeley.edu/~steffen/

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

     objects to See Also as 'gdPlot'

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

     if(interactive()){
     mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
     plusStrand = new("GeneRegion", chromosome = "17", start = 30450000, end = 30550000, strand = "+", biomart = mart)
     genomeAxis = new("GenomeAxis", add53=TRUE)
     gdPlot(list(genomeAxis, plusStrand), minBase = 30450000, maxBase =  30550000)
     }

