Multiple testing on the GO graph package:globaltest R 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 function 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:

       gtGO(..., 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 preformed are passed on
          to 'globaltest'.

      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
     'gtGO' 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:

     'gtGO' cannot be used in combination with the permutation version
     of 'globaltest'.

_A_u_t_h_o_r(_s):

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

_R_e_f_e_r_e_n_c_e_s:

     For references, type: 'citation("globaltest")'. See also the
     vignette GlobalTest.pdf included with this package.

_S_e_e _A_l_s_o:

     Examples in the vignette! 'globaltest', 'GOstructure',
     'gt.multtest'.

_E_x_a_m_p_l_e_s:

         # Breast cancer data (exprSet) from the Netherlands Cancer
         # Institute with small GO structure (all descendants of Cell Cycle)
         # See the vignette for details on making a GO structure object.
         data(vandeVijver)
         data(gostructure.vandeVijver)

         focus <- getFocus(gostructure.vandeVijver)
         adjustedP <- gtGO(vandeVijver, "Surv(TIMEsurvival, EVENTdeath)",
           GO = gostructure.vandeVijver, focus = focus)

         # The significant GO graph can be visualized using
         # the GOstats and Rgraphviz packages.
         # See the vignette for details. Type: vignette("GlobalTest")

