SRSet-class            package:ShortRead            R Documentation

_A _b_a_s_e _c_l_a_s_s _f_o_r _R_o_c_h_e _e_x_p_e_r_i_m_e_n_t-_w_i_d_e _d_a_t_a

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

     This class coordinates phenotype (sample) and sequence data,
     primarily as used on the Roche platform.

     Conceptually, this class has reads from a single experiment
     represented as a long vector, ordered by sample. The 'readCount'
     slot indicates the number of reads in each sample, so that the sum
     of 'readCount' is the total number of reads in the experiment. The
     'readIndex' field is a light-weight indicator of which reads from
     all those available that are currently referenced by the 'SRSet'.

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

     Objects of this class are not usually created directly, but
     instead are created by a derived class, e.g., 'RocheSet'.

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



     '_s_o_u_r_c_e_P_a_t_h': Object of class '"ExperimentPath"', containing the
          directory path where sequence files can be found.

     '_r_e_a_d_I_n_d_e_x': Object of class '"integer"' indicating specific
          sequences included in the experiment.

     '_r_e_a_d_C_o_u_n_t': Object of class '"integer"' conaining the number of
          reads in each sample included in the experiment. The sum of
          this vector is the total number of reads.

     '_p_h_e_n_o_D_a_t_a': Object of class '"AnnotatedDataFrame"' describing
          each sample in the experiment. The number of rows of
          'phenoData' equals the number of elements in 'readCount'.

     '_r_e_a_d_D_a_t_a': Object of class '"AnnotatedDataFrame"' containing
          annotations on all reads.

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

     Class '".ShortReadBase"', directly.

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


     _e_x_p_e_r_i_m_e_n_t_P_a_t_h 'signature(object = "SRSet")': return the
          'ExperimentPath' associated with this object.

     _r_e_a_d_C_o_u_n_t 'signature(object="SRSet")':

     _r_e_a_d_I_n_d_e_x 'signature(object="SRSet")':

     _r_e_a_d_D_a_t_a 'signature(object="SRSet")':

     _s_o_u_r_c_e_P_a_t_h 'signature(object="SRSet")': Retrieve the corresponding
          slot from 'object'.

     _s_h_o_w 'signature(object = "SRSet")': dispaly the contents of this
          object.

     _d_e_t_a_i_l 'signature(object = "SRSet")': provide more extensive
          information on the object.

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

     Michael Lawrence <mflawrence@fhcrc.org>

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

     showClass("SRSet")

