GeneModel-class         package:GenomeGraphs         R Documentation

_C_l_a_s_s "_G_e_n_e_M_o_d_e_l", _r_e_p_r_e_s_e_n_t_s _a _c_u_s_t_o_m _g_e_n_e _m_o_d_e_l

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

     This class represents a custom gene model defined by exon
     boundaries.  An example of this class could be an Affymetrix gene
     model used to create the Affy Exon array

_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("GeneModel",
     ...)'.

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


     '_e_x_o_n_S_t_a_r_t': Object of class '"numeric"', vector containing the
          start positions of the exons that are to be drawn

     '_e_x_o_n_E_n_d': Object of class '"numeric"', vector containing the end
          positions of the exons that are to be drawn 

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

     '_d_p': Object of class '"DisplayPars"', color of the exons and size
          of the exon model in the final plot 

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

     No methods defined with class "GeneModel" in the signature.

_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:

     data("unrData", package="GenomeGraphs")
     affyModel = new("GeneModel", exonStart = unrPositions[,3], exonEnd =  unrPositions[,4])
     gdPlot(list(affyModel), minBase = min(unrPositions[,3]), maxBase=max(unrPositions[,4]))

