GOstats-defunct           package:GOstats           R Documentation

_D_e_f_u_n_c_t _F_u_n_c_t_i_o_n_s _i_n _G_O_s_t_a_t_s _P_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     The functions or variables listed here are no longer part of
     GOstats as they are not needed (any more).

_U_s_a_g_e:

     combGOGraph(g1, g2)
     hyperGtable(probids, lib, type="MF", pvalue=0.05,
                             min.count=10, save = FALSE, output = TRUE,
                             filename = NULL, universe = NULL)
     hyperG2Affy(probids, lib, type="MF", pvalue=0.05,
                              min.count=10, universe = NULL)

_A_r_g_u_m_e_n_t_s:

      g1: A graph

      g2: A graph

 probids: A vector of Affymetrix probe IDs

     lib: An annotation package (e.g., 'hgu95av2.db')

    type: One of "MF", "CC", "BP", indicating molecular function,
          cellular component, or biological process, respectively.

  pvalue: The significance level used to choose GO terms

min.count: The minimum number of a given GO term that must be on the
          chip in order to choose that GO term. This protects against
          very low p-values that result from the situation where there
          are very few genes with a given GO term on the chip, but one
          or two are found in the set of significant genes.

universe: A character vector of unique Entrez Gene identifiers or
          'NULL'.  This is the population (the urn) of the
          Hypergeometric test.  When 'NULL' (default), the population
          is all Entrez Gene ids in the annotation package that have a
          GO term annotation in the specified GO category (see
          'GOHyperG' for more details).

    save: Boolean - Set to 'TRUE' to save the resulting 'data.frame'.

  output: Boolean - Set to 'TRUE' to output the resulting 'data.frame'
          as a text file.

filename: If output is set to 'TRUE', give the file name for the output
          file.

_D_e_t_a_i_l_s:

     'combGOGraph' was replaced by 'join'. 'hyperGtable' was replaced
     by 'summary'. 'hyperG2Affy' was replaced by 'probeSetSummary'.

