expandedProfile          package:goProfiles          R Documentation

_B_u_i_l_d_s _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:

     Expanded profiles are used mainly for comparison of profiles based
     on the theory developed by Sanchez et al (2007) (see references)

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

     expandedProfile(genelist, idType = "Entrez", onto = "ANY", level = 2,orgPackage=NULL, anotPackage=NULL, 
             multilevels = NULL, ord = TRUE, na.rm = TRUE, percentage = TRUE)

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

genelist: List of genes on which the Profile has to be based

  idType: Type of identifiers for the genes. Use 'Entrez' preferably

    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'). This field must be provided if the gene
          list passed to the function is either a character vector of
          'Entrez' (NCBI) identifiers or a character vector of probe
          names

anotPackage: Name of Bioconductor annotations package. This field must
          be provided if the gene list passed to the function is a
          character vector of probe names

     ord: Set to 'TRUE' if the profile has to appear ordered by the
          category names

multilevels: If it is not NULL it must be a vector of GO categories
          that defines the level at where the profile is built

   na.rm: Set to 'TRUE' if NAs should be removed

percentage: Set to 'TRUE' if the profile must be built using
          percentages

_D_e_t_a_i_l_s:

     The function admits three types of entries: Entrez ('Entrez'),
     Bioconductor probe set names ('BioCprobes')  or a special type of
     data frames ('GOTermsFrames'). If the identifier type are
     'BioCprobes'  then an annotation package name must be provided
     too.

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

     An object of class GOProfile containing an expanded profile

_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, Volume 137, Issue 12, Pages 3975-3989, 2007.

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

     basicProfile

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

     data(CD4Ids)
     CD4.Expanded <-expandedProfile(genelist=CD4LLids, onto='MF', level=2, orgPackage="org.Hs.eg.db")

