getEDB                 package:maDB                 R Documentation

_R_e_t_r_i_e_v_i_n_g _e_x_p_r_e_s_s_i_o_n _v_a_l_u_e_s _f_r_o_m _a _d_a_t_a_b_a_s_e.

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

     'getEDB' this function reads the expression values from the
     specified signal channels out of a PostgreSQL database. Micro
     array experiments can be stored into a PostgreSQL database using
     the 'publishToDB' method of the 'EexprSet' object.

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

     getEDB(con,ids,signal.channels.pk,column.names=c("array_name","color"),v=TRUE)

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

     con: A connection object (create it with the dbConnect.PgSQL.conn
          function from the package 'RdbiPgSQL')

     ids: The IDs of the genes from which the expression values should
          be retrieved. In the case of Affymetrix GeneChips the
          Affymetrix IDs should be used (as they are used as rownames
          in the 'exprs' matrix in the 'exprSet' objects).

signal.channels.pk: the primary keys of the signal channels in the
          database from which the expression values should be
          retrieved. To get information about primary keys, arrays...
          from the database use the 'dbGetExperimentInfo' function.

column.names: The information that should be used as column names of
          the expression values matrix. Allowed are all column names of
          the sample database table.

       v: If TRUE additional information will be printed to the
          console.

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

     This function is useful, if one wants to get only a subset of
     genes from a subset of signal channels of one micro array
     experiment out of the database. Alternative functions are the
     'loadFromDB' method of the 'EexprSet' class, or use the
     'dbSendQuery' function of the 'RdbiPgSQL' package in combination
     with SQL.

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

     Johannes Rainer

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

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

     'publishToDB' 'dbGetExperimentInfo' 'loadFromDB' 'getMDB'

