makeARABIDOPSISCHIP_DB     package:AnnotationDbi     R Documentation

_C_r_e_a_t_e_s _a _s_q_l_i_t_e _d_a_t_a_b_a_s_e, _a_n_d _t_h_e_n _m_a_k_e_s _a_n _a_n_n_o_t_a_t_i_o_n _p_a_c_k_a_g_e
_w_i_t_h _i_t

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

     This function 1st creates a SQLite file useful for making a SQLite
     based annotation package by using the correct popXXXCHIP_DB
     function. Next, this function produces an annotation package
     featuring the sqlite database produced.

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

       makeARABIDOPSISCHIP_DB(affy, prefix, fileName, chipMapSrc, chipSrc,
       outputDir, version, manufacturer, chipName, manufacturerUrl)

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

    affy: Boolean to indicate if this is starting from an affy csv file
          or not.  If it is, then that will be parsed to make the
          sqlite file, if not, then you can feed a tab delimited file
          with IDs as was done before with AnnBuilder. 

  prefix: prefix is the first part of the eventual desired package
          name. (ie. "prefix.db") 

fileName: The path and filename for the file to be parsed.  This field
          can be ommitted if affy is set to TRUE.  For all other
          arabidopsis chips, the IDs that match to the probes MUST be
          TAIR IDs. 

chipMapSrc: The path and filename to the intermediate database
          containing the mapping data for allowed ID types and how
          these IDs relate to each other. 

 chipSrc: The path and filename to the intermediate database containing
          the annotation data for the sqlite to build. 

outputDir: Where you would like the output files to be placed. 

 version: What is the version number for the desired package. 

manufacturer: Who made the chip being described. 

chipName: What is the name of the chip. 

manufacturerUrl: URL for manufacturers website. 

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

     ## Not run: 

     ## End(Not run)

