Multiple testing on the GO graphpackage:GlobalAncovaR Documentation

_M_u_l_t_i_p_l_e _t_e_s_t_i_n_g _o_n _t_h_e _G_O _g_r_a_p_h

_D_e_s_c_r_i_p_t_i_o_n:

     Three functions adapted from package 'globaltest' to test (part
     of) the GO graph for association of the gene expression profile of
     GO terms with a response variable. Used together, these functions
     return multiplicity-adjusted p-values calculated using the Focus
     Level procedure that preserves the structure of the GO graph.

_U_s_a_g_e:

       GAGO(..., GO, focus, maxalpha = 0.05, stopafter = 100, verbose = FALSE)
       

_A_r_g_u_m_e_n_t_s:

     ...: Arguments describing the tests to be performed are passed on
          to 'GlobalAncova'.  Note that only the approximative version
          of 'GlobalAncova' is used here and hence the parameter 
          'method' is not available. Even though the number of
          permutations ('perm') may be specified since very large gene
          sets (with more genes than 'max.group.size') are treated with
          the permutation test.

      GO: An object of class 'GOstructure' describing the structure of
          the GO graph. This object should be created using
          'makeGOstructure'.

   focus: A vector of GO ids to describe te focus level. Typically made
          using 'getFocus'.

maxalpha: The maximum multiplicity-adjusted p-value. The algorithm will
          stop when this value is exceeded.

stopafter: The maximum number of significant GO terms to be found. The
          algorithm will stop when this value is exceeded.

 verbose: If set to 'TRUE', prints much more extensive progress
          information.

_D_e_t_a_i_l_s:

     Previous to a call to 'GAGO', first use 'makeGOstructure' to make
     a GO graph tailored to a specific data set. Then 'getFocus' can be
     used to choose a focus level. Finally 'GAGO' performs the focus
     level procedure.

_V_a_l_u_e:

     The function returns a named vector of multiplicity-adjusted
     p-values. Adjusted p-values of GO terms not appearing in this
     vector are larger than the chosen value of 'maxalpha'.

_N_o_t_e:

     Function 'GAGO' corresponds to function 'gtGO' in package
     'globaltest'. The difference is in the use of the 'GlobalAncova'
     test instead of 'globaltest' within the focus level procedure.

_A_u_t_h_o_r(_s):

     Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting; Manuela Hummel

_R_e_f_e_r_e_n_c_e_s:

     Goeman, J.J. and Mansmann, U., Family-wise error rate on the
     directed acyclic  graph of Gene Ontology, submitted.

_S_e_e _A_l_s_o:

     'gtGO', 'GlobalAncova', 'globaltest',  'GOstructure',
     'makeGOstructure', 'getFocus'

_E_x_a_m_p_l_e_s:

       # see vignettes of packages GlobalAncova and globaltest and help of gtGO

