readIntensities          package:ShortRead          R Documentation

_R_e_a_d _S_o_l_e_x_a '_i_n_t' _a_n_d '_n_s_e' _f_i_l_e_s

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

     'readIntensities' reads image `intensity' files (such as Solexa's
     '_int.txt' and (optionally) '_nse.txt') in a directory into a
     single object.

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

     readIntensities(dirPath, pattern=character(0), ...)

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

 dirPath: Directory path or other object (e.g., 'SolexaPath' for which
          methods are defined.

 pattern: A length 1 character vector representing a regular expression
          to be combined (using, e.g., 'paste(pattern, intExtension,
          sep="")' with 'intExtension' or 'nseExtension' to match files
          to be summarized.

     ...: Additional arguments used by methods.

_D_e_t_a_i_l_s:

     Additional methods are defined on specific classes, see, e.g.,
     'SolexaPath'.

     The 'readIntensities,character-method' contains an arugment 'type'
     that determines how intensities are parsed. Use the 'type'
     argument to 'readIntensities,character-method', as follows:



   '_t_y_p_e="_I_p_a_r_I_n_t_e_n_s_i_t_y"' Intensities are read from Solexa '_pos.txt',
        '_int.txt.p', '_nse.txt.p'-style file triplets. The signature
        for this method is

        'dirPath, pattern=character(0), ..., type="IparIntensity",
        intExtension="_int.txt.p.gz", nseExtension="_nse.txt.p.gz",
        posExtension="_pos.txt", withVariability=TRUE, verbose=FALSE'


   '_t_y_p_e="_S_o_l_e_x_a_I_n_t_e_n_s_i_t_y"' Intensities are read from Solexa '_int.txt'
        and '_nse.txt'-style files; see 'SolexaPath' for details.  The
        signature for this method is

        'dirPath, pattern=character(0), ..., type="SolexaIntensity",
        intExtension="_int.txt", nseExtension="_nse.txt",
        withVariability=TRUE, verbose=FALSE'


     Arugments to these methods are as follows:



   _i_n_t_E_x_t_e_n_s_i_o_n, _n_s_e_E_x_t_e_n_s_i_o_n, _p_o_s_E_x_t_e_n_s_i_o_n 'character(1)' values
        pasted (with 'sep=""') to 'pattern' to identify different file
        sources.

   _w_i_t_h_V_a_r_i_a_b_i_l_i_t_y Include estimates of variability (i.e., from parsing
        '_nse' files).

   _v_e_r_b_o_s_e Report on progress when starting to read each file.


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

     An object derived from class 'Intensity'.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     fl <- system.file("extdata", package="ShortRead")
     sp <- SolexaPath(fl)
     int <- readIntensities(sp)
     int
     intensity(int)[1,,]             # one read
     intensity(int)[[1:2,,]]         # two reads, as 'array'
     head(rowMeans(intensity(int)))  # treated as 'array'
     head(pData(readInfo(int)))

