pm.getabst             package:annotate             R Documentation

_O_b_t_a_i_n _t_h_e _a_b_s_t_r_a_c_t_s _f_o_r _a _s_e_t _P_u_b_M_e_d _l_i_s_t.

_D_e_s_c_r_i_p_t_i_o_n:

     The data provided by PubMed is reduced to a small set. This set is
      then suitable for further rendering.

_U_s_a_g_e:

     pm.getabst(geneids, basename)

_A_r_g_u_m_e_n_t_s:

 geneids: The identifiers used to find Abstracts 

basename: The base name of the annotation package to use. 

_D_e_t_a_i_l_s:

     We rely on the annotation in the package associated with the 
     'basename' to provide PubMed identifiers for the genes described
     by the gene identifiers. With these in hand we then use the
     'pmfetch' utility to download the PubMed abstracts in XML form.
     These are then translated (transformed) to a  shorter version
     containing a small subset of the data provided by PubMed.

     This function has the side effect of creating an environment in 
     '.GlobalEnv' that contains the mapping for the requested data.
     This is done for efficiency - so we don't continually read in the
     data when there are many different queries to be performed.

_V_a_l_u_e:

     A list of lists containing objects of class 'pubMedAbst'. There
     will be one element of the list for each identifier. Each of these
     elements is a list containing one abstract (of class 'pubMedAbst'
     for each PubMed identifier associated with the gene identifier.

_A_u_t_h_o_r(_s):

     Robert Gentleman

_S_e_e _A_l_s_o:

     'pm.abstGrep', '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")