genbank               package:annotate               R Documentation

_A _f_u_n_c_t_i_o_n _t_o _o_p_e_n _t_h_e _b_r_o_w_s_e_r _t_o _G_e_n_b_a_n_k _w_i_t_h _t_h_e _s_e_l_e_c_t_e_d _g_e_n_e.

_D_e_s_c_r_i_p_t_i_o_n:

     Given a vector of Genbank accession numbers or NCBI UIDs, the user
     can either have a browser display a URL showing a Genbank query
     for those identifiers, or a XMLdoc object with the same data.

_U_s_a_g_e:

     genbank(...,disp=c("data","browser"), type=c("accession","uid"),
             pmaddress=.pmfetch("Nucleotide", disp, type))

_A_r_g_u_m_e_n_t_s:

     ...: Vectorized set of Genbank accession numbers or NCBI UIDs

    disp: Either "Data" or "Browser" (default is data).  Data returns a
          XMLDoc, while Browser will display information in the user's
          browser.

    type: Denotes whether the arguments are accession numbers or UIDS. 
          Defaults to accession values.

pmaddress: Specific path to the pubmed pmfetch engine from the NCBI
          website.

_D_e_t_a_i_l_s:

     A simple function to retrieve Genbank data given a specific ID,
     either through XML or through a web browser.  This function will
     accept either Genbank accession numbers or NCBI UIDs (defined as a
     Pubmed ID or a Medline ID) - although the types must not be mixed
     in a single call. 

     WARNING:  The powers that be at NCBI have been known to ban the IP
     addresses of users who abuse their servers (currently defined as
     less then 2 seconds between queries).  Do NOT put this function in
     a tight loop or you may find your access revoked.

_V_a_l_u_e:

     If the option "data" is used, an object of type XMLDoc is
     returned, unless there was an error with the query in which case
     an object of type try-error is returned.

     If the option "browser" is used, nothing is returned.

_A_u_t_h_o_r(_s):

     R. Gentleman

_S_e_e _A_l_s_o:

     'pubmed', 'locuslinkByID', 'locuslinkQuery', 'xmlTreeParse'

_E_x_a_m_p_l_e_s:

        ## Use UIDs to get data in both browser & data forms

        if ( interactive() ) {
           disp <- c("data","browser")
        } else {
           disp <- "data"
        }

        for (dp in disp)
          genbank("12345","9997",disp=dp,type="uid")

        ## Use accession numbers to retrieve browser info
        if ( interactive() )
            genbank("U03397","AF030427",disp="browser")