selectLibs             package:SAGElyzer             R Documentation

_F_u_n_c_t_i_o_n_s _t_o _s_u_p_p_o_r_t _t_h_e _w_i_d_g_e_t_s _o_f _S_A_G_E_l_y_z_e_r

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

     SAGElyzer has several widgets that takes inputs from users before
     performing certain tasks. Functions described in this help
     documentation provides supports for the widgets. They may have
     limited reuse values for other purposes.

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

     selectLibs()
     getDBArgs(what = c("map", "counts", "info"))
     getUnixDBArgs(binding = "pg")
     getBinding(binding = c("pg"))
     getWinDBArgs(what = c("map", "counts", "info"))
     getTag()
     getDefaults()
     getSLyzerArgs(argName = "SAGELyzerArgs")
     writeSLyzerArgs(args,argName = "SAGELyzerArgs")
     modSLyzerArgs(argName, value)
     setSLyzerArgs()
     runSLyzer()
     writeSAGEKNN(knn, targetSAGE)
     getSAGEKNN()
     getLibCounts()
     mapLib2File()
     linkTag2UG()
     remapTagNUG(mappings)
     SAGEFromGEO()
     procSAGE()
     mapSAGE2UG()
     showDBError()
     setKNNArgs()
     findNG4Tag()

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

    what: 'what' - a character string that can be "map", "counts", or
          "info" to indicate the database table to be accessed

 binding: 'binding' - a character string for the name of the database
          binding object to be used. "pg" for PostgreSQL is the only
          one that is currently supported

    args: 'args' a list of arguments that will be stored in a
          predefined environment for later usr

 argName: 'argName' a character string for the name of an element in
          the stored list of arguments

   value: 'value' a value to be associated with an element of the
          stored list of arguments

     knn: 'knn' a named vector with the names being the tags that are
          closely related to a given target tag and values being the
          calculated distances

targetSAGE: 'targetSAGE' a character string for the target tag selectd

mappings: 'mappings' a matrix with mappings between SAGE tags and
          UniGene ids

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

     'selectLibs' allows users to select a set of SAGE libraries from
     an interactive interface and store the data in an pre-defined
     environment for later use.

     'getDBArgs' invokes an interactive interface for users to input
     the arguments for making connections to an existing database. User
     inputs are stored in a predefined environment for later use. The
     function calls 'getUnixDBArgs' or 'getWinDBArgs' depending on the
     type of the operating system.

     'getUnixDBArgs' invokes the interface for getting arguments for
     making a connection to a database under Unix. 

     'getWinDBArgs' invokes an interactive interface for getting
     arguments for making a connection to a database under windows
     through an ODBC bridge.

     'getTag' invokes an interfactive interface for users to input the
     target SAGE tag base on which tags with similar expression pattern
     will be sought.

     'getDefaults' invokes an interactive interface for users to reset
     the default values  arguments for 'SAGELyzer'.

     'getSLyzerArgs' returns the argument list stored in a predefined
     environment. 

     'writeSLyzerArgs' overwrites the argument list stored in a
     predefined environment.

     'modSLyzerArgs' modifies the value of a given element of the
     argument list that is stroed in a predefined environment.

     'setSLyzerArgs' initializes the values of the argument list and
     store teh list in a predefined environment for later use.

     'runSLyzer' invokes the function 'SAGELyzer' with correct
     arguments to calculate the nearest neighbor for a given targe tag.

     'writeSAGEKNN' writes the calculated distances for tags that are
     closely related to the target tag to a predefined environment.

     'getSAGEKNN' gets the value for the nearest neighbor of a target
     tag that have been stored in a predefined environment.

     'getLibCounts' invokes the interface to show the actual counts of
     the nearest neighbors of a target tag.

     'mapLib2File' invokes the interface that displays the mapping
     between the column name of the database table for counts and the
     original file name that was used to populate the column.

     'linkTag2UG' invokes an HTML page with links of the tags that are
     closely related to the target tag to UniGene data page for each of
     the tags.

     'remapTagNUG' returns a matrix with each SAGE tag mapped to a
     single UniGene id from a matrix where a tag may be mapped to
     multiple UniGene ids separated by a ";"

     'SAGEFromGEO' invokes the interactive interface to get SAGE
     libraries from the NCBI web site.

     'procSAGE' process SAGE libraries and write the merged data to a
     database table.

     'mapSAGE2UG' invokes an interactive interface for taking inputs
     from users in order to map SAGE tags to UniGene ids and write the
     mappings to a database table.

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

     'getUnixDBArgs' returns a list containing 

  dbname: 'dbname' a character string for the name of the database

    user: 'user' a character string for the name of the user

password: 'password' a character string for a password

    host: 'host' a character string for the domain name or IP address
          of the host for the database

  counts: 'counts' a character string for the name of the databsae
          table storing SGAE count data

    info: 'info' a character string for the name of the database table
          storing mapping information and normalization data

     map: 'map' a character string for the name of the database table
          storing the mappings between tag and UniGene ids

     DSN: 'DSN' a character string for the name of data source name

  counts: 'counts' a character string for the name of the databsae
          table storing SGAE count data

    info: 'info' a character string for the name of the database table
          storing mapping information and normalization data

     map: 'map' a character string for the name of the database table
          storing the mappings between tag and UniGene ids


     'getSLyzerArgs' returns a list of arguments that is stroed in a
     predefined environment.

     'getSAGEKNN' returns a named vector with tag names and their
     distances to a target tag.

     'remapTagNUG' returns a matrix with two columns.

_N_o_t_e:

     The functions are part of the Bioconductor project at Dana-Farber
     Cancer Institute to provide Bioinformatics functionalities through
     R

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

     Jianhua Zhang

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

     <URL: http://www.ncbi.nlm.nih.gov/geo>

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

     'SAGELyzer', 'mergeSAGE'

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

     ## No examples are provided as the functions may require the support of
     ## database or human interference

