read.cel.complete         package:affxparser         R Documentation

_P_a_r_s_i_n_g _a_n _A_f_f_y_m_e_t_r_i_x _C_E_L _f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Parsing an Affymetrix CEL file using the Fusion SDK. The 
     intention is to let users obtain all (but possibly a subset of)
     information in the CEL file.

_U_s_a_g_e:

     read.cel.complete(fname, indices = NULL, read.intensities = TRUE,
                       read.stdvs = TRUE, read.pixels = TRUE,
                       read.xy = FALSE, read.outliers = TRUE,
                       read.masked = TRUE, verbose = 0)

_A_r_g_u_m_e_n_t_s:

   fname: the name of the CEL file.

 indices: a vector of indices indicating which features to read. If the
          argument is 'NULL' all features will be returned.

read.intensities: a logical: will the intensities be returned.

read.stdvs: a logical: will the standard deviations be returned.

read.pixels: a logical: will the number of pixels be returned.

 read.xy: a logical: will the (x,y) coordinates be returned.

read.outliers: a logical: will the outliers be return.

read.masked: a logical: will the masked features be returned.

 verbose: how verbose do we want to be. 0 is no verbosity, higher
          numbers mean more verbose output. At the moment the values 1
          and 2 are supported.

_D_e_t_a_i_l_s:

     This function reads everything from a CEL file. It is considered a
     bug if the file contains information not accessible by this
     function, please report it.

     The (input and output) interface makes heavily use of the concept
     of indices. An (x,y) coordinate is converted to an integer by the
     formula (y + 1) times numberOfColsInCelFile + (x + 1), assuming
     that the (x,y) coordinates start at (0,0).

     The file returns a list with components (possible empty depending
     on the input flags) corresponding to the various flags. The
     'outliers' and 'masked' components are special in that they are
     vectors of indices of features flagged as respectively
     outlier/masked by the Affymetrix image software.

_V_a_l_u_e:

     A named list with components described below. The order of the
     'intensities', 'stdvs' and 'pixels' corresponds to the ordering of
     the 'indices' argument. 

  header: The header of the CEL file. Equivalent to the output from
          'read.cel.header', see the documentation for that function.

intensities: A vector of mode 'nummeric' containing the intensity
          associated with each feature, unless 'read.intensities =
          FALSE' in which case it will be 'NULL'. Restricted to
          features  within the 'indices' range.

   stdvs: A vector of mode 'nummeric' containing the standard deviation
          associated with each feature, unless 'read.stdvs = FALSE' in
          which case it will be 'NULL'. Restricted to features within
          the 'indices' range.

  pixels: A vector of mode 'integer' containing the number of pixels
          associated with each feature, unless 'read.pixels = FALSE' in
          which case it will be 'NULL'. Restricted to features within
          the 'indices' range.

       x: A vector of mode 'integer' containing the x coordinate
          associated with each feature, unless 'read.xy = FALSE' in
          which case it will be 'NULL'. Restricted to features with the
          'indices' range.

       y: A vector of mode 'integer' containing the y coordinate
          associated with each feature, unless 'read.xy = FALSE' in
          which case it will be 'NULL'. Restricted to features with the
          'indices' range.

outliers: A vector of mode 'integer' which the indices of the features
          flagged as outliers, unless 'read.outliers = NULL' in which
          case it will be 'NULL'. Note that there is a difference
          between 'outliers = NULL' and 'outliers = integer(0)' - the
          last case happens when 'read.outliers = TRUE' but there are
          no outliers. In case an 'indices' argument is given, only
          indices within the 'indices' argument are returned.

  masked: A vector of mode 'integer' which the indices of the features
          flagged as masked, unless 'read.masked = NULL' in which case
          it will be 'NULL'. Note that there is a difference between
          'masked = NULL' and 'masked = integer(0)' - the last case
          happens when 'read.masked = TRUE' but there are no masked
          features. In case an 'indices' argument is given, only
          indices within the 'indices' argument are returned.

_N_o_t_e:

     Memory usage: the Fusion SDK allocates memory for the entire CEL
     file, when the file is accessed (but does not actually read the
     file into memory). Using the 'indices' argument will therefore
     only affect the memory use of the final object (as well as speed),
     not the memory allocated in the C function used to parse the file.
     This should be a minor problem however.

     The outlier/masked flag are computed by the Affymetrix image
     analysis software. The current community view seems to be that
     this should be done based on statistical modelling of the actual
     probe intensities and should be based on the choice of
     preprocessing algorithm. Mopst algorithms are only using the
     intensities from the CEL file.

_A_u_t_h_o_r(_s):

     James Bullard, bullard@stat.berkeley.edu and Kasper Daniel Hansen,
     khansen@stat.berkeley.edu

_S_e_e _A_l_s_o:

     'affxparserInfo' for a package overview and 'read.cel.header' for
     a description of the header output. Often a user only wants to
     read the intensities, look at 'read.cel.intensities' for a
     function specialized for that use. See 'xy2indices' from 'affy'
     and 'xy2i' from 'makePlatformDesign' for a discussion of the index
     approach.

_E_x_a_m_p_l_e_s:

     ## Not run: 
     read.cel.complete("~/testFile.CEL", read.npixels = FALSE)
     ## End(Not run)

