hyperGtable             package:GOstats             R Documentation

(_D_E_P_R_E_C_A_T_E_D) _T_a_b_l_e _f_r_o_m _G_O_H_y_p_e_r_G

_D_e_s_c_r_i_p_t_i_o_n:

     Use the 'summary' method on a 'GOHyperGResult' object.

     Output a table from a call to 'GOHyperG'.

_U_s_a_g_e:

     hyperGtable(probids, lib, type = "MF", pvalue = 0.05, min.count = 10,
     save = FALSE, output = TRUE, filename = NULL, 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.

    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.

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:

     This function will take a vector of Affymetrix IDs and output a
     'data.frame' containing information on all GO terms that are found
     significant in a call to 'GOHyperG'.

_V_a_l_u_e:

     A 'data.frame' containing the following columns:

     GO Term - The GOID associated with a given GO term

     Description - The description for that GO term

     p-values - The p-value associated with that GO term

     Number significant - The number of genes in the vector of
     Affymetrix IDs with that particular GO term

     Number on chip - The number of genes on the Affymetrix chip with
     that particular GO term.

_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]
     hyperGtable(probids, "hgu95av2", save = TRUE, output = FALSE)
     ## End(Not run)

