getGEOfile             package:GEOquery             R Documentation

_D_o_w_n_l_o_a_d _a _f_i_l_e _f_r_o_m _G_E_O _s_o_f_t _f_i_l_e _t_o _t_h_e _l_o_c_a_l _m_a_c_h_i_n_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function simply downloads a SOFT format file associated with
     the GEO accession number given.

_U_s_a_g_e:

     getGEOfile(GEO, destdir = tempdir(), amount = c("full", "brief", "quick", "data"))

_A_r_g_u_m_e_n_t_s:

     GEO: Character string, the GEO accession for download (eg., GDS84,
          GPL96, GSE2553, or GSM10)

 destdir: Directory in which to store the resulting downloaded file. 
          Defaults to tempdir()

  amount: Amount of information to pull from GEO.  Only applies to GSE,
          GPL, or GSM.  See details... 

_D_e_t_a_i_l_s:

     This function downloads GEO SOFT files based on accession number. 
     It does not do any parsing.  The first two arguments should be
     fairly self-explanatory, but the last is based on the input to the
     acc.cgi url at the geo website.  In the default "full" mode, the
     entire SOFT format file is downloaded.  Both "brief" and "quick"
     offer shortened versions of the files, good for "peeking" at the
     file before a big download on a slow connection.  Finally, "data"
     downloads only the data table part of the SOFT file and is good
     for downloading a simple EXCEL-like file for use with other
     programs (a convenience).

_V_a_l_u_e:

     Invisibly returns the full path of the downloaded file.

_A_u_t_h_o_r(_s):

     Sean Davis

_R_e_f_e_r_e_n_c_e_s:

     http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi

_S_e_e _A_l_s_o:

     'getGEO'

_E_x_a_m_p_l_e_s:

       myfile <- getGEOfile('GDS2')