getAE              package:ArrayExpress              R Documentation

_D_o_w_n_l_o_a_d _M_A_G_E-_T_A_B _f_i_l_e_s _f_r_o_m _A_r_r_a_y_E_x_p_r_e_s_s _i_n _a _s_p_e_c_i_f_i_e_d _d_i_r_e_c_t_o_r_y

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

     'getAE' downloads and extracts the MAGE-TAB files from an
     ArrayExpress dataset.

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

     getAE(input, path = ".", type = "full", extract = TRUE)

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

   input: is an ArrayExpress identifier. 

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

    type: can be 'raw' to download and extract only the raw data,
          'processed' to download and extract only the processed data
          or 'full' to have both raw and processed data.

 extract: if FALSE, the files are not extracted from the zip archive.

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

     ' A list with the names of the files that have been downloaded and
     extracted. '

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

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

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

     'magetab2bioc', 'getcolproc'

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

     mexp1422 = getAE("E-MEXP-1422", type = "full")

     ## Build a an ExpressionSet from the raw data
     MEXP1422raw = magetab2bioc(files = mexp1422)

     ## Build a an ExpressionSet from the processed data
     cnames = getcolproc(mexp1422)
     MEXP1422proc = procset(mexp1422, cnames[2])

