processData           package:PAnnBuilder           R Documentation

_C_o_n_v_e_r_t _D_a_t_a _F_o_r_m_a_t

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

     Convert data format by R function, or produce perl program to
     process data.

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

     getBaseParsers(baseMapType, db=FALSE)

     fileMuncher(outName, dataFile, parser, organism)
     fileMuncher_DB(dataFile, parser, organism)

     writeInput(parser, perlName, organism, dataFile)
     writeInputSP(perlName,organism)
     writeInputIPI(perlName,organism)
     writeInputREFSEQ(perlName,organism)
     writeInputBLAST(perlName,organism, dataFile)
     writeInputPFAM(perlName,organism)
     writeInputINTERPRO(perlName,organism)
     writeOutput(parser, perlName)
     .callPerl(script, os)

     getSrcObjs(srcUrls, organism, built, fromWeb = TRUE)
     getBaseData(srcObjs)

     splitEntry(dataRow, sep = ";", asNumeric = FALSE)
     twoStepSplit(dataRow, entrySep = ";", eleSep = "@", asNumeric = FALSE)
     mergeRowByKey(mergeMe, keyCol = 1, sep = ";")

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

baseMapType: a character string to indicate which database will be 
          parsed. It can be "sp","trembl","ipi","refseq","equal",
          "merge","mppi", "PeptideAtlas","DBSubLoc","Pfam", "pfamname"
          or "blast".

      db: a boolean to indicate whether the parser file for the
          SQLite-based  package will be returned. 

 outName: a character string for the output file name of perl program.

dataFile: a character string for the input file name of perl program.

  parser: a character string for the path of the parser file.

organism: a character string for the name of the organism of concern.
          (eg: "Homo sapiens")

perlName: a character string for the name of perl program.

  script: a character string for the name of perl program.

      os: character string, giving the Operating System (family) of 
          the computer.

 srcUrls: character string, giving the url of concerned database.

   built: a character string for the release/version information of
          source data.

 fromWeb: a boolean to indicate whether the source data will be 
          downloaded from the web or read from a local file

 srcObjs: a object of class "pBase". 

 dataRow: character vector, each element of which is to be split.

     sep: a character string containing regular expression(s) to use as
           "split". 

asNumeric: a boolean to indicate whether the elements will be 
          converted to objects of type "numeric".

entrySep: a character string containing regular expression(s) to use 
          in the first "split". 

  eleSep: a character string containing regular expression(s) to use 
          in the second "split". 

 mergeMe: a vector or a matrix which duplicating values for the same id
          will be merged

  keyCol: a integer indicating the column index to be regarded as key.

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

     These functions are from Bioconductor "AnnBuilder" package, but
     add many  new operations depend on the requirements of building
     proteomic annotation  data packages.

     'getBaseParsers' return a character string of the name of a 
     parser file based on the given database. Each parser file is a
     part of  perl script and used to parse relevant data.

     'fileMuncher' produce perl file based on given parser and 
     additional input files, then perform this perl program via R. 
     'fileMuncher_DB' produce perl file based on given parser and 
     additional input, then perform this perl program via R. Result
     data are  stored in the relative ouput files. It is designed for
     the SQLite-based annotation package. 'writeInput' write additional
     information including input files  into the perl script.
     'writeOutput' write information about ouput files into the perl 
     script. '.callPerl' perform perl program via R.

     'getSrcObjs' given url of database and concerned organism,  define
     objects of class "pBase". pBase is a sub class of "pubRepo", and
     it  is used for SwissProt, TREMBL, IPI and NCBI RefSeq data. 
     'getBaseData' get basic protein annotation data and sequence  data
     from protein database: SwissProt, TREMBL, IPI, NCBI PefSeq.

     'splitEntry' split multiple entry for a given mapping.
     'twoStepSplit' split multiple entry with two separaters  (e.g.
     12345@18;67891@18). 'mergeRowByKey' merge duplicating values for
     the same key.

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

     'getBaseParsers' returns the path of parser file.

     'getSrcObjs' returns a list of defined the objects of class 
     "pBase".

     'getBaseData' returns a matrix of protein annotation data.

     'splitEntry' returns a vector.

     'twoStepSplit' returns a vector.

     'mergeRowByKey' returns a data frame containing the merged values.

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

     Hong Li

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

     Zhang, J., Carey, V., Gentleman, R. (2003) An extensible
     application for  assembling annotation for genomic
     data.Bioinformatics 19(1), 155-156.

