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)
       makeGOstructure(data, annotation, top, only.ids, ontology = c("BP", "CC", "MF"), unreliable)
       getFocus(GOstructure, maxatoms = 10)

_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.

    data: The data set for which the 'GOstructure' object is to be
          made. Can be either an 'exprSet' or a vector of probe
          indicators.

annotation: The name of the metaData annotation package to be used, or
          a vector of EntrezGene ids with the same length as the number
          of genes in 'data'.

     top: The node to be used as top node of the 'GOstructure'.
          Defaults to one of "GO:0008150", "GO:0005575", "GO:0003674",
          depending on he ontology chosen. The 'GOstructure' object
          will only contain offspring of the chosen top node.

only.ids: A vector of GO ids. If this is supplied, GO ids not appearing
          in this list will not appear in the 'GOstructure' object.

ontology: The ontology to be used. One of Biological Process (BP),
          Cellular Component (CC) or Molecular Function (MF).

unreliable: Can be used to designate one or more of the GO evidence
          codes as unreliable. Value must be a vector containing one or
          more from "IC", "IDA", "IEA", "IEP", "IGI", "IMP", "IPI",
          "ISS", "NAS", "ND", "RCA", "TAS", "NR".

GOstructure: An object of class 'GOstructure'.

maxatoms: A tuning parameter that governs the choice of the focus
          level. 'getFocus' will choose those GO terms in the focus
          level in such a way that all offspring gene sets of each
          focus level term can be constructed as unions of no more than
          'maxatoms' atom gene sets. Default value of 'maxatoms' is 10.
          Higher values quickly lead to slower computation. Lower
          values typically lead to reduced power.

_D_e_t_a_i_l_s:

     These functions should be used in the following order. 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'

_E_x_a_m_p_l_e_s:

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

