isValidKey             package:annotate             R Documentation

_G_e_t _o_r _v_e_r_i_f_y _v_a_l_i_d _I_D_s _f_o_r _a _p_a_c_k_a_g_e.

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

     These functions either verify that a list of IDs are primary and
     valid IDs for a package, or else return all the valid primary IDs
     from a package

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

     isValidKey(ids, pkg)
     allValidKeys(pkg)

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

     ids: A character vector containing IDs that you wish to validate.

     pkg: The package name of the chip for which we wish to validate
          IDs.

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

     Every package has some kind of ID that is central to that package.
     For chip-based packages this will be some kind of probe, and for
     the organism based packages it will be something else (usually an
     entrez gene ID).  isValidKey takes a list of IDs and tests to see
     whether or not they are present (valid) in a particular package. 
     allValidKeys simply returns all the valid primary IDs for a
     package.

_V_a_l_u_e:

     'isValidKey' returns a vector of TRUE or FALSE values
     corresponding to whether or not the ID is valid.

     'allValidKeys' returns a vector of all the valid primary IDs.

_A_u_t_h_o_r(_s):

     Marc Carlson

_S_e_e _A_l_s_o:

     'updateSymbolsToValidKeys'

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

     ## Not run: 
       ## 2 bad IDs and a 3rd that will be valid
       ids <- c("15S_rRNA_2","21S_rRNA_4","15S_rRNA")
       isValidKey(ids, "org.Sc.sgd")

       ## 2 good IDs and a 3rd that will not be valid
       ids <- c("5600","7531", "altSymbol")
       isValidKey(ids, "org.Hs.eg")

       ## Get all the valid primary id from org.Hs.eg.db
       allValidKeys("org.Hs.eg")
     ## End(Not run)

