compareProfilesLists       package:goProfiles       R Documentation

_C_o_m_p_a_r_e_s _t_w_o _o_f _e_x_p_a_n_d_e_d _p_r_o_f_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function compares two lists (``sensu R lists'') of expanded
     profiles by successive  calls to function
     \texttt{compareGOProfiles} following  the methodology developed by
     Sanchez, Salicru and Ocan\~a (2007)

_U_s_a_g_e:

     compareProfilesLists(expanded1, expanded2, common.expanded=NULL, relationType,
     method = "lcombChisq", ab.approx = "asymptotic", confidence = 0.95, ...)

_A_r_g_u_m_e_n_t_s:

expanded1: First expanded profile to be compared

expanded2: Second expanded profile to to be compared

common.expanded: Expanded profile made from the genes appearing in both
          lists of genes

relationType: Type of relation between gene lists compared through the
          expanded profiles. It can be INCLUSION, INTERSECTION or
          DISJOINT

  method: The approximation method to the sampling distribution under
          the null hypothesis specifying that the samples pn and qm
          come from the same population. See the 'Details' section
          below

confidence: The confidence level of the confidence interval in the
          result

ab.approx: The approximation used for computing 'a' and 'b'
          coefficients (see details)

     ...: Other arguments for the methods 'basicProfile' or
          'compareGoProfiles'

_V_a_l_u_e:

     The result of the comparison is a list with a variable number of
     arguments, depending for which ontologies has been performed the
     comparison. Each list member is an object of class 'htest'
     corresponding to the output of the function 'compareGOProfiles'

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

     Alex Sanchez

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

     Sanchez-Pla, A., Salicru, M. and Ocana, J. Statistical methods for
     the analysis of high-throughput data based on functional profiles
     derived from the gene ontology. Journal of Statistical Planning
     and Inference, 2007

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

     'compareGeneLists', 'expandedProfile'

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

     require(goProfiles)
     data(sampleProfiles)
     comparedMF<- compareProfilesLists (expandedWelsh01, expandedSingh01, relationType="DISJOINT")
     print(comparedMF)
     print(compSummary(comparedMF))

