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(), AnnotGPL = FALSE, 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()

AnnotGPL: A boolean defaulting to FALSE as to whether or not to use the
          Annotation GPL information.  These files are nice to use
          because they contain up-to-date information remapped from
          Entrez Gene on a regular basis.  However, they do not exist
          for all GPLs; in general, they are only available for GPLs
          referenced by a GDS

  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('GDS10')

