amplicon.plot          package:geneplotter          R Documentation

_C_r_e_a_t_e _a_n _a_m_p_l_i_c_o_n _p_l_o_t

_D_e_s_c_r_i_p_t_i_o_n:

     Given a two-sample test statistic and an ExpressionSet this
     function plots regions of the genome that are either highly
     expressed (in red) or have low expression (blue) differentially in
     the two groups.

_U_s_a_g_e:

     amplicon.plot(ESET, FUN, genome)

_A_r_g_u_m_e_n_t_s:

    ESET: an object of class 'ExpressionSet'

     FUN: A two sample test function suitable for 'esApply'. 

  genome: A character string of the base name for the annotation. 

_D_e_t_a_i_l_s:

     In some genetic studies we are interested in finding regions of
     the genome where there are a set of highly expressed genes in some
     subgroup of the population. This set of highly (or lowly)
     expressed genes is often of great interest. For example in breast
     cancer the HER-2 gene is on an amplicon. In some patients
     approximately 5 genes located near HER-2 are all amplified.

     These plot should help in the search for such regions.

_V_a_l_u_e:

     No value is returned. This function is executed purely for side
     effect.

_A_u_t_h_o_r(_s):

     Robert Gentleman

_S_e_e _A_l_s_o:

     'esApply', 'make.chromOrd'

_E_x_a_m_p_l_e_s:

       ##none yet; takes too long

