DAVIDQuery            package:DAVIDQuery            R Documentation

_D_A_V_I_D_Q_u_e_r_y

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

     Launch a query against DAVID, the Database for Annotation,
     Visualization and Integrated Discovery.  Return the results into
     an R object.

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

     DAVIDQuery(ids = "O00161,O75396", type = "UNIPROT_ACCESSION", annot, tool, URLlengthLimit = 2048,
     details = TRUE, verbose = FALSE, writeHTML = FALSE, testMe = FALSE, graphicMenu = FALSE,  formatIt = TRUE)

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

     ids: IDs for desired objects, as a character vector or as a single
          string with ids separated by ",".  To be passed to the DAVID
          website, the format has to be the latter.

    type: Type of input ids. If missing, a menu is contructed from the
          R object DAVIDTypeChoices.  See <URL:
          http://david.abcc.ncifcrf.gov/content.jsp?file=DAVID_API.html#input_list>
          for up-to-date choices.  

   annot: Type of annotation requested. If missing, a menu is
          contructed from the R object DAVIDAnnotChoices.  See <URL:
          http://david.abcc.ncifcrf.gov/content.jsp?file=DAVID_API.html#input_list>
          for up-to-date choices.  

    tool: Type of gene tool to use. If missing, a menu is contructed
          from the R object DAVIDToolChoices.  See <URL:
          http://david.abcc.ncifcrf.gov/content.jsp?file=DAVID_API.html#input_list>
          for up-to-date choices.  As of this writing, the tool choices
          corresponding to the Functional Annotation tools cannot be
          handled by this package. 

URLlengthLimit: Published maximum length of the constructed URL. 

 details: If TRUE (default), a list of intermediate results is
          returned;  otherwise, just the final query result. 

 verbose: If TRUE (default is FALSE), more debugging information is
          printed. 

writeHTML: If TRUE (default is FALSE), write the received intermediate
          HTML to files. 

  testMe: If TRUE (default is FALSE), assign default valuse and run. 

graphicMenu: If TRUE (default is FALSE), use a GUI window for the pick
          menus. 

formatIt: If TRUE (default), try to interpret the returned character
          table and structure the result. If false, the unadorned
          character table returned by DAVID.

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

     The API described at <URL:
     http://david.abcc.ncifcrf.gov/content.jsp?file=DAVID_API.html> is
     used.  The return is screen-scraped, a new URL is formulated and
     transmitted, again the return is screen-scraped to find the name
     of the results file, and finally that file is retrieved into a
     string matrix.  

     Obviously this approach is brittle, but it has survived the 2008
     DAVID update. A real API would be better, of course.

     The return value DAVIDQueryResult is just a character matrix.  Its
     content structure depends on the choices of tool and annotation
     arguments, so there has been no attempt to manipulate it into,
     say, a data frame with nice column names.

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

     If detail==FALSE, only DAVIDQueryResult is returned. This a
     character matrix holding the results of the tab-delimited file
     returned by DAVID.

     If detail==TRUE, a list with contents useful for trouble-shooting: 

firstURL: 

firstStageResult: 

DAVIDaction: 

secondURL: 

secondStageResult: 

hasSessionEnded: 

downloadFileName: 

downloadURL: 

DAVIDQueryResult: 

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

     Roger Day

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://david.abcc.ncifcrf.gov> <URL:
     http://david.abcc.ncifcrf.gov/content.jsp?file=DAVID_API.html>
     Article:    DAVID gene ID conversion tool.   Da Wei Huang, Brad T
     Sherman, Robert Stephens, Michael W Baseler, H Clifford Lane, and
     Richard A Lempicki <URL:
     http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18841237>

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

     'DAVIDQueryLoop', 'formatDAVIDResult'

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

     result = DAVIDQuery(testMe=TRUE)$DAVIDQueryResult
     print(length(result))
     print(result$firstURL)
     print(result$secondURL)
     print(result$O00161$REFSEQ_MRNA)  ### Uses UNIPROT ID's for input.

