goSlim-methods           package:GSEABase           R Documentation

_M_e_t_h_o_d_s _f_o_r _F_u_n_c_t_i_o_n _g_o_S_l_i_m _i_n _P_a_c_k_a_g_e _G_S_E_A_B_a_s_e

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

     These methods summarize the gene ontology terms implied by the
     'idSrc' argument into the GO terms implied by the 'slimCollection'
     argument. The summary takes identifiers in 'idSrc' and determines
     all GO terms that apply to the identifiers. This full list of GO
     terms are then classified for membership in each term in the
     'slimCollection'.

     The resulting object is a data frame containing the terms of
     'slimCollection' as row labels, counts and frequencies of
     identifiers calssified to each term, and an abbreviated term
     description.

     An identifier in 'idSrc' can expand to serveral GO terms, and the
     GO terms in 'slimCollection' can imply an overlapping hierarchy of
     terms. Thus the resulting summary can easily contain more counts
     than there are identifiers in 'idSrc'.

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

     goSlim(idSrc, slimCollection, ontology, ..., verbose=FALSE)

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

   idSrc: An argument determining the source of GO terms to be mapped
          to slim terms. The source might be a 'GOCollection' of terms,
          or another object (e.g., ExpressionSet) for which the method
          can extract GO terms.

slimCollection: An argument containing the GO slim terms.

ontology: A character string nameing the ontology to be consulted when
          identifing slim term hierarchies. One of MF (molecular
          function), BP (biological process), CC (cellular
          compartment).

     ...: Additional arguments passed to specific emthods.

 verbose: Logical influencing whether messages (primarily missing GO
          terms arising during creation of the slim hierarchy) are
          reported.

_M_e_t_h_o_d_s:


     _i_d_S_r_c="_G_O_C_o_l_l_e_c_t_i_o_n", _s_l_i_m_C_o_l_l_e_c_t_i_o_n="_G_O_C_o_l_l_e_c_t_i_o_n", _o_n_t_o_l_o_g_y="_c_h_a_r_a_c_t_e_r", ..., _v_e_r_b_o_s_e=_F_A_L_S_E 
          Classify 'idSrc' GO terms into 'slimCollection' categories.
          The hierarchy of terms included for each term is from the
          ontology (MF, BP, or CC) specified by 'ontology'. 'verbose'
          informs about, e.g., GO terms that are not found.

     _i_d_S_r_c="_E_x_p_r_e_s_s_i_o_n_S_e_t", _s_l_i_m_C_o_l_l_e_c_t_i_o_n="_G_O_C_o_l_l_e_c_t_i_o_n", _o_n_t_o_l_o_g_y="_c_h_a_r_a_c_t_e_r", ...,  _v_e_r_b_o_s_e=_F_A_L_S_E 
          Determine the (unique) GO terms implied by feature names in
          'idSrc' (using the annotation map identified in
          'annotation(idSrc)').

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

     myIds <- c("GO:0016564", "GO:0003677", "GO:0004345", "GO:0008265",
                "GO:0003841", "GO:0030151", "GO:0006355", "GO:0009664",
                "GO:0006412", "GO:0015979", "GO:0006457", "GO:0005618",
                "GO:0005622", "GO:0005840", "GO:0015935", "GO:0000311")
     myCollection <- GOCollection(myIds)
     fl <- system.file("extdata", "goslim_plant.obo", package="GSEABase")
     slim <- getOBOCollection(fl)
     goSlim(myCollection, slim, "MF")
     data(sample.ExpressionSet)
     goSlim(sample.ExpressionSet, slim, "MF", evidenceCode="TAS")

