checkForDifferentAnnotation       package:maDB       R Documentation

_D_e_t_e_c_t _g_e_n_e _a_n_n_o_t_a_t_i_o_n _d_i_f_f_e_r_e_n_c_e_s

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

     'checkForDifferentAnnotation' compares the gene annotation in the
     'annotation' database table with the gene annotation provided by
     the specified R annotation package. The IDs which differ in the
     annotation are returned in a table.

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

     checkForDifferentAnnotation(con,chip,check.columns=c("GenBank","UniGene","LocusLink"),v=TRUE)

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

     con: The connection object to the database (Connections can be
          opened with the 'dbConnect' function from the 'RdbiPgSQL'
          package).

    chip: The chip for which the annotation should be checked. At the
          moment only Affymetrix chips are supported (eg.
          'hgu133plus2').

check.columns: The identifiers that should be compared for the genes
          (Affymetrix probe sets).

       v: if some additional informations should be written to the
          console.

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

     This function compares the annotation for the genes (or Affymetrix
     probe set IDs) that are available in a database table called
     'annotation' and the corresponding R annotation package (like the
     'hgu133plus2' package). The annotation IDs specified by the
     'check.columns' attribute from the two different sources are
     compared for each gene and if they differ the gene and the
     different annotations are returned.

_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:

     'dbUpdateAnnotation' 'dbGetAnnotation'

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

