RocheSet-class           package:ShortRead           R Documentation

_R_o_c_h_e (_4_5_4) _e_x_p_e_r_i_m_e_n_t-_w_i_d_e _d_a_t_a _c_o_n_t_a_i_n_e_r

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

     This class is meant to coordinate all data in a Roche (454)
     experiment. See 'SRSet' for additional details.

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

     Create objects from this class using one of the 'RocheSet' methods
     documented below

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



     '_s_o_u_r_c_e_P_a_t_h': Object of class '"RochePath"' The file system
          location of the data used in this experiment.

     '_r_e_a_d_I_n_d_e_x': Object of class '"integer"' indexing reads included
          in the experiment; see 'SRSet' for details on data
          representation in this class.

     '_r_e_a_d_C_o_u_n_t': Object of class '"integer"' containingn the number of
          reads associated with each sample; see 'SRSet' for details on
          data representation in this class.

     '_p_h_e_n_o_D_a_t_a': Object of class '"AnnotatedDataFrame"' with as many
          rows as there are samples, containing information on
          experimental design.

     '_r_e_a_d_D_a_t_a': Object of class '"AnnotatedDataFrame"' containing as
          many rows as there are reads, containing information on each
          read in the experiment.

_E_x_t_e_n_d_s:

     Class '"SRSet"', directly. Class '".Roche"', directly. Class
     '".ShortReadBase"', by class "SRSet", distance 2. Class
     '".ShortReadBase"', by class ".Roche", distance 2.

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

     No methods defined with class "RocheSet" in the signature; see
     'SRSet' for inherited methods.

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

     Michael Lawrence <mflawrence@fhcrc.org>

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

     'SRSet'

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

     showClass("RocheSet")

