getQueryLink            package:annotate            R Documentation

_F_u_n_c_t_i_o_n_s _t_o _c_r_e_a_t_e _h_y_p_e_r_t_e_x_t _l_i_n_k_s _t_h_a_t _c_a_n _b_e _p_l_a_c_e_d _i_n _a _t_a_b_l_e
_c_e_l_l _o_f _a _H_T_M_L _f_i_l_e

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

     Given a vector of ids, the functions will create a vector of
     hypertext links to a defined public repositories such as
     LocusLink, UniGene .... The linkages can be placed in a html file
     constructed by 'htmlpage'

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

     getQueryLink(ids, repository = "ug")
     getTDRows(ids, repository = "ug")
     getCells(ids, repository = "ug")
     getQuery4LL(ids)
     getQuery4UG(ids)
     getQuery4SP(ids)
     getQuery4GB(ids)
     getQuery4OMIM(ids)
     getQuery4Affy(ids)
     getQuery4FB{ids}
     getQuery4EN(ids)

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

     ids: A character vector of ids, or alternatively, a list
          containing character vectors of ids. These will be used to
          construct hypertext links. A list should be used in cases
          where there are multiple ids per gene.

repository: A character string for the name of a public repository.
          Valid values include "ll", "ug", "gb", "sp", "omim", "affy",
          "en", and "fb". 

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

     'getQuery4LL' constructs hypertext links to LocusLink using the
     provided ids.

     'getQuery4GB' constructs hypertext links to GenBank using the
     provided ids.

     'getQuery4UG' constructs hypertext links to UniGene using the
     provided ids.

     'getQuery4Affy' constructs hypertext links to Affymetrix using the
     provided ids.

     'getQuery4SP' constructs hypertext links to SwissProt using the
     provided ids.

     'getQuery4OMIM' constructs hypertext links to OMIM using the
     provided ids.

     'getQuery4FB' constructs hypertext links to FlyBase using the
     provided ids.

     'getQuery4EN' constructs hypertext links to EntrezGene using the
     provided ids. This supercedes 'getQuery4LL', as LocusLink has been
     deprecated by NCBI.

     'getQueryLink' directs calls to construct hypertext links using
     the provided ids.

     'getTDRows' constructs each row of the resulting table.

     'getCells' constructs each cell of the resulting table.

     Note that some of these functions ('getQuery4OMIM', 'getQuery4UG',
     'getQuery4LL'), 'getQuery4FB' attempt to return empty cells for
     ids that don't make sense, rather than broken links. For the other
     getQuery4XX functions, the end user must replace all nonsense ids
     with "&nbsp;" in order to have an empty cell.

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

     Returns a vector of character strings representing the hypertext
     links.

_N_o_t_e:

     The functions are part of Bioconductor project at Dana-Farber
     Cancer Institute to provide Bioinformatics functionalities through
     R

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

     Jianhua Zhang <jzhang@jimmy.harvard.edu> with further
     modifications by James W. MacDonald <jmacdon@med.umich.edu>

