affyParaIntern           package:affyPara           R Documentation

_I_n_t_e_r_n_a_l _a_f_f_y_P_a_r_a _o_b_j_e_c_t_s / _f_u_n_c_t_i_o_n_s

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

     Internal functions for the 'affyPara' package.

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

     initAffyBatchSF(object, object.type)

     getAffyBatchSF()
     getIntensitySF(rows, refindexname)
     getCompIntensitySF(rows)
     getCompIntensityMatrixSF(rows, drop=FALSE)
     getFUNAffyBatchSF(FUN)

     createDirSF(to, showWarnings = TRUE, recursive = TRUE)
     writeLinesSF(data, fileName)
     listFilesSF(path, full.names=TRUE)
     ReadHeader(object)

     file.name(file, fsep = .Platform$file.sep)

     getObjectType(object)
     checkPartSize(object, number.parts)

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

  object: An object of class AffyBatch OR a 'character' vector with the
          names of CEL files OR a (partitioned) list of 'character'
          vectors with CEL file names.

object.type: Declaration for the type of the argument 'object':
          "AffyBatch", "CELfileVec", "partCELfileList" 

    rows: Number of rows which have to be changed. 

refindexname: The name of the array used as a reference. 

    drop: A logical value. If 'TRUE' the dimensions of an array which
          have only one level will be deleted. 

     FUN: A function generating a value from a an AffyBatch. e.g. 'dim' 

      to: A 'character' vector, that defines the path and name of the
          new directory.

showWarnings: A logical value; should the warnings on failure be shown?

recursive: A logical values; should elements of the path other than the
          last be created? If 'TRUE', like Unix's mkdir -p.

    data: A 'character' vector, containing the data for the file.

fileName: A 'character' string with the file name.

    path: A 'character' vector with the full directory.

full.names: A logical value. If 'TRUE', the directory path is prepended
          to the file names. If 'FALSE', only the file names are
          returned.

    file: A 'character' vector of file names with prepended directory
          path.

    fsep: A 'character' string, giving the file separator used on your
          platform. 

number.parts: Number of nodes in the computer cluster.

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

     Internal functions for the 'affyPara' package. The functions have
     to be used in a cluster function (e.g. clusterApply) from the SNOW
     package.

'_i_n_i_t_A_f_f_y_B_a_t_c_h_S_F' Slavefunction for initializing an AffyBatch at
     slaves. AffyBatch will be stored in the .GlobalEnv with the name
     'AffyBatch'.

'_g_e_t_A_f_f_y_B_a_t_c_h_S_F' Slavefunction to get an AffyBatch from slaves. Gets
     the object AffyBatch from the .GlobalEnv. 

'_g_e_t_I_n_t_e_n_s_i_t_y_S_F' Slavefunction to get special values from the intensity
     matrix from slaves.

'_g_e_t_C_o_m_p_I_n_t_e_n_s_i_t_y_S_F' Slavefunction to get special rows from the
     intensity matrix from slaves.

'_g_e_t_C_o_m_p_I_n_t_e_n_s_i_t_y_M_a_t_r_i_x_S_F' Slavefunction to get complete intensity
     matrix from slaves.

'_g_e_t_F_U_N_A_f_f_y_B_a_t_c_h_S_F' Slavefunction to get a value from an AffyBatch at
     slaves.

'_c_r_e_a_t_e_D_i_r_S_F' Slavefunction to create a directory at slaves.

'_w_r_i_t_e_L_i_n_e_s_S_F' Slavefunction to write data into a file at slaves.

'_l_i_s_t_F_i_l_e_s_S_F' Slavefunction to list files from directory at slaves.

'_R_e_a_d_H_e_a_d_e_r' Slavefunction to return Header-Informations from CEL Files
     at slaves. 

'_f_i_l_e._n_a_m_e' Function to get file name from a 'character' with complete
     file path (directory path and filename).

'_g_e_t_O_b_j_e_c_t_T_y_p_e' Function to get type from object.

'_c_h_e_c_k_P_a_r_t_S_i_z_e' Function to check object for length.

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

     Markus Schmidberger schmidb@ibe.med.uni-muenchen.de, Ulrich
     Mansmann mansmann@ibe.med.uni-muenchen.de

