neighborGeneFinder         package:annotate         R Documentation

_A _w_i_d_g_e_t _f_o_r _l_o_c_a_t_i_n_g _g_e_n_e_s _n_e_i_g_h_b_o_r_i_n_g _a _t_a_r_g_e_t _g_e_n_e

_D_e_s_c_r_i_p_t_i_o_n:

     Given a set of data (matrix) with entries for LocusLink or UniGene
     ids, the neighboring genes of a gene selected from a list on the
     interface can be located.

_U_s_a_g_e:

     neighborGeneFinder(geneData, keyName = c("unigene", "locuslink"),
     organism = c("human", "mouse", "rat")) 

_A_r_g_u_m_e_n_t_s:

geneData: 'geneData' a matrix with columns named. The name for one of
          the columns has to be either "locuslink" or "unigene"

 keyName: 'keyName' a character string for the name of the key columns
          of 'geneData'. Has to be either "locuslink" or "unigene"

organism: 'organism' a character string for the name of the organism of
          interest. Has to be "human", "mouse", or "rat"

_D_e_t_a_i_l_s:

     Bioconductor's data package XXXCHRLLOC has to be instatlled for
     the widget to work. If 'keyName' is "unigene", XXXLLMappings is
     required, where XXX is the name of the organism of interest.

_V_a_l_u_e:

     This function returns a list of lists. Elements of the top level
     list are either LocusLink or UniGene ids. A sublist is inturn a
     list of lists whose top level elements are chromosome numbers,
     each of which is a list with an "upstream" and "downstream"
     elements.

_N_o_t_e:

     This function is part of the Bioconductor project at Dana-Farber
     Cancer Institute to provide Bioinformatics functionalities through
     R

_A_u_t_h_o_r(_s):

     Jianhua Zhang

_E_x_a_m_p_l_e_s:

       if(interactive()){
          require("annotate", character.only = TRUE) ||
          stop("Package annotate is not availble")
          geneData <- cbind(paste("100", 1:16, "_at", sep = ""), c(1, 50,
                            10044, 51, 71, 51371, 81, 51426, 188, 293, 360,
                            364, 375, 387, 513, 10572))
          colnames(geneData) <- c("Probe", "locuslink")
          neighborGeneFinder(geneData, "locuslink", "human")
       }