pm.abstGrep             package:annotate             R Documentation

_A_n _i_n_t_e_r_f_a_c_e _t_o _g_r_e_p _f_o_r _P_u_b_M_e_d _a_b_s_t_r_a_c_t_s.

_D_e_s_c_r_i_p_t_i_o_n:

     A user friendly interface to the functionality provided by
     'pubmed'.

_U_s_a_g_e:

     pm.abstGrep(pattern, absts, ...)

_A_r_g_u_m_e_n_t_s:

 pattern: A pattern for the call to 'grep'. 

   absts: A list containing abstracts downloaded using 'pubmed' or
          equivalent. 

     ...: Extra arguments passed to 'grep'. 

_D_e_t_a_i_l_s:

     The 'absts' are a list of PubMed XML objects that have been
     downloaded  and parsed. This function lets the user quickly search
     the abstracts for any regular expression. The returned value is a
     logical vector indicating which of the abstracts contain the
     regular expression.

_V_a_l_u_e:

     The returned value is a logical vector indicating which of the
     abstracts contain the regular expression.

_A_u_t_h_o_r(_s):

     Robert Gentleman

_S_e_e _A_l_s_o:

     'pm.getabst', 'pm.titles'

_E_x_a_m_p_l_e_s:

       hoxa9 <- "37809_at"

        ## 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) ) {
          absts <- pm.getabst(hoxa9, "hgu95av2")

          pm.abstGrep("NUP98", absts[[1]])

          pm.abstGrep("apoptosis", absts[[1]])
       }