SolexaIntensity          package:ShortRead          R Documentation

_C_o_n_s_t_r_u_c_t _o_b_j_e_c_t_s _o_f _c_l_a_s_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:

     These function constructs objects of 'SolexaIntensity' and
     'SolexaIntensityInfo'. It will often be more convenient to create
     these objects using parsers such as 'readIntensities'.

_U_s_a_g_e:

     SolexaIntensity(intensity=array(0, c(0, 0, 0)),
                     measurementError=array(0, c(0, 0, 0)),
                     readInfo=SolexaIntensityInfo(
                       lane=integer(nrow(intensity))),
                     ...)
     SolexaIntensityInfo(lane=integer(0),
                         tile=integer(length(lane)),
                         x=integer(length(lane)),
                         y=integer(length(lane)))

_A_r_g_u_m_e_n_t_s:

intensity: A matrix of image intensity values. Successive columns
          correspond to nucleotides A, C, G, T; four successive columns
          correspond to each cycle. Typically, derived from
          '"_int.txt"' files.

measurementError: As 'intensity', but measuring standard error. Usually
          derived from '"_nse.txt"' files.

readInfo: An object of class 'AnnotatedDataFrame', containing
          information described by 'SolexaIntensityInfo'.

    lane: An integer vector giving the lane from which each read is
          derived.

    tile: An integer vector giving the tile from which each read is
          derived.

       x: An integer vector giving the tile-local x coordinate of the
          read from which each read is derived.

       y: An integer vector giving the tile-local y coordinate of the
          read from which each read is derived.

     ...: Additional arguments, not currently used.

_V_a_l_u_e:

     An object of class 'SolexaIntensity', or 'SolexaIntensityInfo'.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     'SolexaIntensity'.

