dropECode              package:annotate              R Documentation

_D_r_o_p _G_O _l_a_b_e_l_s _f_o_r _s_p_e_c_i_f_i_e_d _E_v_i_d_e_n_c_e _C_o_d_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Genes are mapped to GO terms on the basis of evidence codes. In
     some analyses it will be appropriate to drop certain sets of
     annotations based on specific evidence codes.

_U_s_a_g_e:

     dropECode(inlist, code="IEA")

_A_r_g_u_m_e_n_t_s:

  inlist: A list of GO data 

    code: The set of codes that should be dropped. 

_D_e_t_a_i_l_s:

     A simple use of 'lapply' and 'sapply' to find and eliminate those
     terms that have the specified evidence codes.

     This might be used when one is using to GO to validate a sequence
     matching experiment (for example), then all terms whose mapping
     was based on sequence similarity (say ISS and IEA) should be
     removed.

_V_a_l_u_e:

     A list of the same length as the input list retaining only those
     annotations whose evidence codes were not the ones in the
     exclusion set 'code'.

_A_u_t_h_o_r(_s):

     R. Gentleman

_S_e_e _A_l_s_o:

     'getEvidence', 'getOntology'

_E_x_a_m_p_l_e_s:

     library("GO")
      bb=GOENTREZID2GO$"4121"
      getEvidence(bb[1:3])
      cc = dropECode(bb[1:3])
      if (length(cc))
        getEvidence(cc)