Intensity-class          package:ShortRead          R Documentation

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_c_l_a_s_s_e_s _f_o_r _s_h_o_r_t _r_e_a_d _i_m_a_g_e _i_n_t_e_n_s_i_t_i_e_s

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

     The 'Intensity', 'IntensityMeasure', and 'IntensityInfo' classes
     represent and manipulate image intensity measures. Instances from
     the class may also contain information about measurement errors,
     and additional information about the reads from which the
     intensities are derived.

     'Intensity', and 'IntensityMeasure', are virtual classes, and
     cannot be created directly. Classes derived from
     'IntensityMeasure' (e.g., 'ArrayIntensity') and 'Intensity' (e.g.,
     'SolexaIntensity') are used to represent specific technologies.

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

     'ArrayIntensity' objects can be created with calls of the form
     'ArrayIntensity(array(0, c(1,2,3)))'.

     Objects of derived classes can be created from calls such as the
     'SolexaIntensity' constructor, or more typically by parsing
     appropriate files (e.g., 'readIntensities').

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

     Class 'Intensity' has slots:



     '_r_e_a_d_I_n_f_o': Object of class '"IntensityInfo"' containing columns
          for the lane, tile, x, and y coordinates of the read.

     '_i_n_t_e_n_s_i_t_y': Object of class '"IntensityMeasure"' containing image
          intensity data for each read and cycle.

     '_m_e_a_s_u_r_e_m_e_n_t_E_r_r_o_r': Object of class '"IntensityMeasure"'
          containing measures of image intensity uncertainty for each
          read and cycle.

     '._h_a_s_M_e_a_s_u_r_e_m_e_n_t_E_r_r_o_r': Length 1 logical variable indicating
          whether intensity standard errors are included (internal use
          only).


     Classes 'IntensityInfo' and 'IntensityMeasure' are virtual
     classes, and have no slots.

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

     These classes extend '".ShortReadBase"', directly.

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

     Methods and accessor functions for 'Intensity' include:



     _r_e_a_d_I_n_f_o 'signature(object = "Intensity")': access the 'readInfo'
          slot of 'object'.

     _i_n_t_e_n_s_i_t_y 'signature(object = "Intensity")': access the
          'intensity' slot of 'object'.

     _m_e_a_s_u_r_e_m_e_n_t_E_r_r_o_r 'signature(object = "Intensity")': access the
          'nse' slot of 'object', or signal an error if no standard
          errors are available.

     _d_i_m 'signature(object = "Intensity")': return the dimensions
          (e.g., number of reads by number of cycles) represented by
          'object'.

     _s_h_o_w 'signature(object = "Intensity")': provide a compact
          representation of the object.


     Subsetting '"["' is available for the 'IntensityMeasure' class;
     the 'drop' argument to '"["' is ignored.

     Subsetting with '"[["' is available for the 'ArrayIntensity'
     class. The method accepts three arguments, corresponding to the
     read, base, and cycle(s) to be selected. The return value is the
     array (i.e., underlying data values) corresponding to the selected
     indices.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     'readIntensities'

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

     showMethods(class="Intensity", where=getNamespace("ShortRead"))
     example(readIntensities)

