PMIDAmat              package:annotate              R Documentation

_A _f_u_n_c_t_i_o_n _t_o _c_o_m_p_u_t_e _t_h_e _p_r_o_b_e _t_o _P_u_b_M_e_d _i_d _i_n_c_i_d_e_n_c_e _m_a_t_r_i_x.

_D_e_s_c_r_i_p_t_i_o_n:

     For a given chip or a given set of genes, it computes the mapping
     from probes to PubMed id.

_U_s_a_g_e:

     PMIDAmat(pkg, gene=NULL)

_A_r_g_u_m_e_n_t_s:

     pkg: The package name of the chip for which the incidence matrix
          should be computed.

    gene: A character vector of interested probe set ids or NULL
          (default).

_D_e_t_a_i_l_s:

     Not much to say, just find which probes are associated with which
     PubMed ids and return the incidence matrix, with PubMed ids as
     rows and probes as columns. 

     To specify a set of probes to use, let the argument 'gene' to be a
     vector of probe ids.   Bt this way, the calculations are not
     involved with non-interested genes/PubMed ids so that the whole
     process could finish soon.

_V_a_l_u_e:

     A matrix containing zero or one, depending on whether the probe
     (column) is associated with a PubMed id (row).

_A_u_t_h_o_r(_s):

     R. Gentleman

_E_x_a_m_p_l_e_s:

       if(require("hgu95av2") ) {
         probe <- names(as.list(hgu95av2ACCNUM))
         Amat = PMIDAmat("hgu95av2", gene=sample(probe, 10))
      }

