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=c("MF","BP","CC") )
     contents(object)

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

       x: The identifiers to be mapped (usually manufacturer)

    data: A character string identifying the data source 

   which: For 'getGOdesc' indicates which GO hierarchy to use.

  object: The environment (data table) that you want to get all
          contents from

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

     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' the
     input vector is GO identifiers (not manufacturer identifiers) and
     in the output any identifier that does not have a description in
     the selected GO hierarchy (MF, BP or CC) is dropped.

_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:

     'multiget'

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

       data(eset)
       gN <- geneNames(eset)[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.
        curWarn <- getOption("warn")
        options(warn=0)
        on.exit(options(warn=curWarn), add=TRUE)
       if( require("hgu95av2", character.only=TRUE)
            && require("GO", character.only=TRUE) ) {
           getSYMBOL(gN,"hgu95av2" )
           gg<- getGO(gN, "hgu95av2")
           getGOdesc(gg[[2]], "MF")
           getLL(gN, "hgu95av2")
           getPMID(gN, "hgu95av2")
       } else
        cat("could not run all examples\n")

