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 " " 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>