makeHUMANCHIP_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:

       makeHUMANCHIP_DB(affy, prefix, fileName, otherSrc, chipMapSrc, chipSrc,
       baseMapType, outputDir, version, manufacturer, chipName,
       manufacturerUrl, author, maintainer)

_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 can
          either be an affy csv file or it can be a more classic file
          type. 

otherSrc: The path and filenames to any other lists of IDs which might
          add information about how a probe will map.   

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. 

baseMapType: The type of ID that is used for the initial base mapping. 
          If using a classic base mapping file, this should be the ID
          type present in the fileName.  This can be any of the
          following values: "gb" = for genbank IDs "ug" = unigene IDs
          "eg" = Entrez Gene IDs "refseq" = refseq IDs "gbNRef" =
          mixture of genbank and refseq IDs 

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. 

  author: List of authors involved in making the package. 

maintainer: List of package maintainers with email addresses for
          contact purposes. 

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

     ## Not run: 
     makeHUMANCHIP_DB(affy = TRUE,
                      prefix = "hgu95av2",
                      fileName = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/hgu95av2/HG_U95Av2_annot.csv.070824",
                      otherSrc = c(
                        EA="/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/hgu95av2/hgu95av2.EA.txt",
                        UMICH="/mnt/cpb_anno/mcarlson/proj/sqliteGen/srcFiles/hgu95av2/hgu95av2_UMICH.txt"),
                      chipMapSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipmapsrc_human.sqlite",
                      chipSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipsrc_human.sqlite",
                      baseMapType = "gbNRef",
                      version = "1.0.0",
                      manufacturer = "Affymetrix",
                      chipName = "hgu95av2",
                      manufacturerUrl = "http://www.affymetrix.com")
     ## End(Not run)

