getGOTerm              package:annotate              R Documentation

_F_u_n_c_t_i_o_n_s _t_o _A_c_c_e_s_s _G_O _d_a_t_a.

_D_e_s_c_r_i_p_t_i_o_n:

     These functions provide access to data in the GO package. The data
     are assembled from publically available data from the Gene
     Ontology Consortium (GO), <URL: www.go.org>. Given a list of GO
     identifiers they access the children (more specific terms), the
     parents (less specific terms) and the terms themselves.

_U_s_a_g_e:

     getGOTerm(x)
     getGOParents(x)
     getGOChildren(x)
     getGOOntology(x)

_A_r_g_u_m_e_n_t_s:

       x: A character vector of valid GO identifiers. 

_D_e_t_a_i_l_s:

     GO consists of three (soon to be more) specific hierarchies:
     Molecular Function (MF), Biological Process (BP) and Cellular
     Component (CC). For more details consult the GO website. For each
     GO identifier each of these three hierarchies is searched and
     depending on the function called the appropriate values are
     obtained and returned.

     It is possible for a GO identifier to have no children or for it
     to have no parents. However, it must have a term associated with
     it.

_V_a_l_u_e:

     A list of the same length as 'x'. The list contains one entry for
     each element of 'x'. That entry is itself a list. With one
     component named 'Ontology' which has as its value one of MF, BP or
     CC. The second component has the same name as the suffix of the
     call, i.e. Children, Parents, or Term. If there was no match in
     any of the ontologies then a length zero list is returned for that
     element of 'x'.

     For 'getGOOntology' a vector of categories (the names of which are
     the original GO term names). Elements of this list that are 'NA'
     indicate term names for which there is no category (and hence they
     are not really term names).

_A_u_t_h_o_r(_s):

     R. Gentleman

_R_e_f_e_r_e_n_c_e_s:

     The Gene Ontology Consortium

_E_x_a_m_p_l_e_s:

      library(GO)

      sG <- c("GO:0005515", "GO:0000123", "GO:0000124", "GO:0000125",
                  "GO:0000126", "GO:0020033", "GO:0006830", 
                  "GO:0015916")

      gT <- getGOTerm(sG)

      gP <- getGOParents(sG)

      gC <- getGOChildren(sG)

      gcat <- getGOOntology(sG)