compareGeneLists         package:goProfiles         R Documentation

_C_o_m_p_a_r_e_s _t_w_o _l_i_s_t_s _o_f _g_e_n_e_s _b_y _b_u_i_l_d_i_n_g (_e_x_p_a_n_d_e_d) _p_r_o_f_i_l_e_s _a_n_d _c_o_m_p_a_r_i_n_g _t_h_e_m

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

     This function wraps all the needed steps to compare two lists of
     genes following  the methodology developed by Sanchez, Salicru and
     Ocan\~a (2007)

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

     compareGeneLists(genelist1, genelist2, idType = "Entrez", onto = "ANY",
     level = 2, orgPackage, 
     method = "lcombChisq", ab.approx = "asymptotic", confidence = 0.95, compareFunction="compareGOProfiles", ...)

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

genelist1: First gene set to be compared

genelist2: Second gene set to be compared

  idType: Type of identifiers for the genes. May be 'Entrez' (default),
          BiocProbes or GoTermsFrame. See the 'Details' section below

    onto: Ontology on which the profile has to be built

   level: Level of the ontology at which the profile has to be built

orgPackage: Name of a Bioconductor's organism annotations package
          ('org.Xx-eg-db')

  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)

compareFunction: Allows to use 'fitGOProfile' (sample vs population) or
          'compareGOProfiles' (sample1 vs sample2)

     ...: 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:

     'compareGOProfiles', 'basicProfile'

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

     data(prostateIds)
     prostateCompared<- compareGeneLists (welsh01EntrezIDs[1:500],
     singh01EntrezIDs[1:500], level=2, onto='MF', orgPackage="org.Hs.eg.db")
     print(prostateCompared)
     print(compSummary(prostateCompared))

