getSYMBOL              package:annotate              R Documentation

_F_u_n_c_t_i_o_n_s _t_o _d_e_a_l _w_i_t_h _D_a_t_a _P_a_c_k_a_g_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     The functions documented here are intended to make it easier to
     map from a set of manufacturers identifiers (such as you will get
     from the chips etc) to other identifiers.

_U_s_a_g_e:

     getSYMBOL(x, data)
     getLL(x, data)
     getGO(x, data)
     getPMID(x, data)
     getGOdesc(x, which)
     lookUp(x, data, what)
     getUniqAnnItem()

_A_r_g_u_m_e_n_t_s:

       x: The identifiers to be mapped (usually manufacturer)

    data: The basename of the meta-data package to be used. 

    what: 'what' a character string for the name of an annotation
          element of an annotation data package

   which: 'which' a character string in the form of MF, BP, CC, or ANY
          to indicated the GO categories of interest

_D_e_t_a_i_l_s:

     Users must supply the basename of the meta-data package that they
     want to use to provide the mappings. The name of the meta-data
     package is the same as the basename.

     Appropriate translations are done. In some cases such as 'getLL'
     and 'getSYMBOL' there will only be one match and a vector is
     returned. In other cases such as 'getPMID' and 'getGO' there may
     be multiple matches and a list is returned.

     For 'getGOdesc' 'x' contains GO identifiers (not manufacturer
     identifiers) and the output is a list of GOTerms objects, if
     'which' specifies some subset of the ontologies (MF, BP or CC) 
     then only terms for that ontology are retained.

     'lookUp' is a general function that can be used to look up
     matches. All other translation functions use 'lookUp'

     A BioC annotation data package contains annotation data
     environments whose names are package name (e. g. hgu95av2) +
     element name (e. g. PMID). 'what' must be one of the element names
     for the given data package. 

     'getUniqAnnItem' keeps track of the annotation elements that have
     one to one mappings.

_V_a_l_u_e:

     Either a vector or a list depending on whether multiple values per
     input are possible.

_A_u_t_h_o_r(_s):

     R. Gentleman

_S_e_e _A_l_s_o:

     'mget'

_E_x_a_m_p_l_e_s:

       data(sample.exprSet.1)
       gN <- geneNames(sample.exprSet.1)[100:105]
        ## A bit of a hack to not have a package dependency on hgu95av2
        ## but need to fiddle w/ the warn level to not fail the example
        ## anyways.
        have_hgu95av2 <- suppressWarnings(require("hgu95av2"))
        have_GO <- suppressWarnings(require("GO"))
        if (have_hgu95av2 && have_GO) {
           lookUp(gN, "hgu95av2", "SYMBOL")
           # Same as lookUp for SYMBOL except the return is a vector
           getSYMBOL(gN,"hgu95av2" )
           gg <- getGO(gN, "hgu95av2")
           lookUp(gg[[2]][[1]][["GOID"]], "GO", "TERM")
           # Same as lookUp for TERM
           getGOdesc(gg[[2]][[1]][["GOID"]], "ANY")
           # For BP only
           getGOdesc(gg[[2]][[1]][["GOID"]], "BP")
           getLL(gN, "hgu95av2")
           getPMID(gN, "hgu95av2")
        } else {
          cat("could not run all examples\n")
        }