basicProfile           package:goProfiles           R Documentation

_B_u_i_l_d_s _b_a_s_i_c _f_u_n_c_t_i_o_n_a_l _p_r_o_f_i_l_e

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

     Compute basic functional profile for a given list of genes/GO
     identifiers, a given ontology at a given level of the GO

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

     basicProfile(genelist, idType = "Entrez", onto = "ANY", level = 2,orgPackage=NULL, anotPackage=NULL, 
             ord = TRUE, multilevels = NULL, empty.cats = TRUE, cat.names = TRUE, na.rm = FALSE)

_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. May be 'Entrez' (default),
          BiocProbes or GoTermsFrame (see details 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'). 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's microarray 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

empty.cats: Set to 'TRUE' if empty categories should appear in the
          profile

cat.names: Set to 'TRUE' if the profile has to contain the names of
          categories

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

_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 (one or more data frames in a list
     named by the ontologies)

_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:

     expandedProfile

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

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

