hyperG2Affy             package:GOstats             R Documentation

(_D_E_P_R_E_C_A_T_E_D) _A _L_i_s_t _o_f _A_f_f_y_m_e_t_r_i_x _I_D_s _f_r_o_m _G_O_I_D_s

_D_e_s_c_r_i_p_t_i_o_n:

     Use 'probeSetSummary' instead.

     Output a list of Affymetrix IDs associated with each significant
     GOID, based on the output from hyperGtable.

_U_s_a_g_e:

     hyperG2Affy(probids, lib, type = "MF", pvalue = 0.05, min.count = 10,
     universe = NULL)

_A_r_g_u_m_e_n_t_s:

 probids: A vector of Affymetrix probe IDs

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

    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).

_D_e_t_a_i_l_s:

     The function 'hyperGtable' will output a table listing a set of
     GOIDs that are significantly over-represented in a set of
     significant genes. The next logical step might be to look at the
     individual genes that are represented by each GOID. This function
     will output the Affymetrix IDs for each GOID in a list, which can
     then be used to either output HTML tables using 'probes2table', or
     possibly just output the gene names for each GOID.

_V_a_l_u_e:

     A named 'list' with all the Affymetrix IDs associated with each
     significant GOID.

_A_u_t_h_o_r(_s):

     James W. MacDonald <jmacdon@med.umich.edu>

_E_x_a_m_p_l_e_s:

     ## Not run: 
     library("hgu95av2")
     probids <- ls(hgu95av2GENENAME)[1:10]
     hyperG2Affy(probids, "hgu95av2")
     ## End(Not run)

