magetab2bioc          package:ArrayExpress          R Documentation

_C_o_n_v_e_r_t _T_A_B-_M_A_G_E _d_a_t_a _i_n_t_o _a _B_i_o_c_o_n_d_u_c_t_o_r _o_b_j_e_c_t

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

     'magetab2bioc' converts local MAGE-TAB files into a AffyBatch, an
     ExpressionSet or a NChannelSet.

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

     magetab2bioc(rawfiles, sdrf, idf, adf, path = ".", rawcol = NULL, save = TRUE)

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

rawfiles: all the expression files to use to create the object. The
          content of the raw.zip MAGE-TAB file.

    sdrf: the sdrf file from MAGE-TAB. 

     idf: the idf file from MAGE-TAB. 

     adf: the adf file from MAGE-TAB. 

    path: is the name of the directory in which the files downloaded on
          the ArrayExpress repository will be extracted.

  rawcol: by default, the columns are automatically selected according
          to the scanner type. If the scanner is unknown or if the user
          wants to use different columns than the default, the argument
          'rawcol' can be set. For two colour arrays it must be a list
          with the fields 'R', 'G', 'Rb' and 'Gb' giving the column
          names to be used for red and green foreground and background.
          For one colour arrays, it must be a character string with the
          column name to be used. These column names must correspond to
          existing column names of the expression files.

    save: if TRUE, the files downloaded from the database will not be
          deleted from path after executing the function.

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

     An object of class 'AffyBatch' or  'ExpressionSet' or 
     'NChannelSet' with the raw expression values in the assayData of
     the object, the information contained in the .sdrf file in the
     phenoData, the adf file content in the featureData and the idf
     file content in the experimentData.

     If several array designs are used in the data set, the output is a
     list with an object for each array design.

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

     Audrey Kauffmann  Maintainer: <audrey@ebi.ac.uk>

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

     'queryAE', 'getAE', 'ArrayExpress'

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

     MEXP1422 = getAE("E-MEXP-1422")
     MEXP1422set = magetab2bioc(rawfiles = MEXP1422$rawfiles, sdrf = MEXP1422$sdrf, idf = MEXP1422$idf, adf = MEXP1422$adf)

