SolexaIntensity-class       package:ShortRead       R Documentation

_C_l_a_s_s_e_s "_S_o_l_e_x_a_I_n_t_e_n_s_i_t_y" _a_n_d "_S_o_l_e_x_a_I_n_t_e_n_s_i_t_y_I_n_f_o"

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

     Instances of 'Intensity' and 'IntensityInfo' for representing
     image intensity data from Solexa experiments.

_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 to 'SolexaIntensityInfo' or
     'SolexaIntensity', or more usually 'readIntensities'.

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

     Object of 'SolexaIntensity' have slots:



     '_r_e_a_d_I_n_f_o': Object of class '"SolexaIntensityInfo"' representing
          information about each read.

     '_i_n_t_e_n_s_i_t_y': Object of class '"ArrayIntensity"' containing an
          array of intensities with dimensions read, base, and cycle.
          Nucleotide are A, C, G, T for each cycle.

     '_m_e_a_s_u_r_e_m_e_n_t_E_r_r_o_r': Object of class '"ArrayIntensity"' containing
          measurement errors for each read, cycle, and base, with
          dimensions like that for 'intensity'. 

     '._h_a_s_M_e_a_s_u_r_e_m_e_n_t_E_r_r_o_r': Object of class '"ScalarLogical"' used
          internally to indicate whether measurement error information
          is included.

     Object of 'SolexaIntensityInfo' 



     _d_a_t_a Object of class '"data.frame"', inheritted from
          'AnnotatedDataFrame'.

     _v_a_r_M_e_t_a_d_a_t_a Object of class '"data.frame"', inheritted from
          'AnnotatedDataFrame'.

     _d_i_m_L_a_b_e_l_s Object of class '"character"', inheritted from
          'AnnotatedDataFrame'.

     '.___c_l_a_s_s_V_e_r_s_i_o_n__' Object of class '"Versions"', inheritted from
          'AnnotatedDataFrame'.

     ._i_n_i_t Object of class '"ScalarLogical"', used internally to
          indicate whether the user initialized this object.


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

     Class 'SolexaIntensity':

     Class '"Intensity"', directly. Class '".ShortReadBase"', by class
     "Intensity", distance 2.

     Class 'SolexaIntensityInfo':

     Class '"AnnotatedDataFrame"', directly Class '"IntensityInfo"',
     directly Class '"Versioned"', by class "AnnotatedDataFrame",
     distance 2 Class '".ShortReadBase"', by class "IntensityInfo",
     distance 2  Class '"IntensityInfo"', directly.

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

     Class "SolexaIntensity" inherits accessor and display methods from
     class 'Intensity'. Additional methods include:



     '[' 'signature(x = "SolexaIntensity", i="ANY", j="ANY", k="ANY")': 

          Selects the ith read, jth nucleotide, and kth cycle.
          Selection is coordinated across intensity, measurement error,
          and read information.


     Class "SolexaIntensityInfo" inherits accessor, subsetting, and
     display methods from class 'IntensityInfo' and
     'AnnotatedDataFrame'.

_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:

     showClass("SolexaIntensity")
     sp <- SolexaPath(system.file('extdata', package='ShortRead'))
     int <- readIntensities(sp)
     int                             # SolexaIntensity
     readInfo(int)                   # SolexaIntensityInfo
     int[1:5,,]                      # read 1:5

