formatDAVIDResult         package:DAVIDQuery         R Documentation

_F_o_r_m_a_t _t_h_e _c_h_a_r_a_c_t_e_r _t_a_b_l_e _r_e_t_u_r_n_e_d _b_y _D_A_V_I_D.

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

     These functions attempt to format the character table 'result'
     returned by DAVID.

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

     formatDAVIDResult(result, verbose=FALSE)
     formatAnnotationReport(result)
     formatGeneReport(result)
     formatGeneReportFull(result)
     formatList(result)
     formatGene2Gene(result)

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

  result: Character table returned by DAVID. 

 verbose: If TRUE, print tool. Warn if tool=="geneReportFull" that the
          result will be returned invisibly due to its size. 

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

     'formatDAVIDResult' switches out to one of 'formatGeneReport', 
     'formatGeneReportFull', 'formatGene2Gene', or 'formatList',
     depending on the 'tool' argument of 'DAVIDQuery()'  used to
     specify what query report to do.  The 'tool' argument is passed as
     an attribute attached to 'result'.

     WARNINGS: Not all values of 'tool' have an associated format.

     These format utilities are not guaranteed to work correctly for
     all combinations of inputs into 'DAVIDQuery()', or to continue to
     work correctly if or when the DAVID API changes.  If results
     appear incorrect, one can use the option
     'DAVIDQuery(formatIt=FALSE)' to see the unformatted output, and/or
     paste 'DAVIDQuery(details=TRUE)[firstURL]' into a browser. 

     In the case of formatGene2Gene, the 'gene' column of the 'details'
     component might not always contain a single identifier.

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

     For 'tool=="geneAnnotationReport"', a list, one component for each
     element in the 'ids' arg. Each component has subcomponents  

Gene Name : Self-explanatory.

Species : Self-explanatory.

   <id> : The identifier(s) in the query. The name is whatever the id
          type was.

<other items> : Items produced for the input, specified by the 'annot'
          arg of the query.   

<gene name> : Using the same ID type as the 'type' argument of
          'DAVIDQuery()'.

Gene Name : Self-explanatory.

Species : Self-explanatory.

Gene Name : Self-explanatory.

Species : Self-explanatory.

<other items> : The union of items produced for the input identifiers
          (generically called "genes" in DAVID).  (The set of
          attributes is not fixed.) 

 median : See DAVID documentation.

    geo : See DAVID documentation.

diagram : An attempt to parse the fourth column of the Functional Group
          line of the input.  See DAVID documentation and consult the
          DAVID team.

details : A data frame with columns 

          _g_e_n_e "gene" as identified in the 'ids' arg to 'DAVIDQuery'

          _g_e_n_e_N_a_m_e gene name

          _u_r_l The URL for the Gene Report page at NIAID.

     As of this writing, the tool choices corresponding to most
     Functional Annotation tools cannot be handled by this package.

