conversionFunctions        package:goProfiles        R Documentation

_F_u_n_c_t_i_o_n_s _t_o _t_r_a_n_s_f_o_r_m_c_o_n_v_e_r_t _o_b_j_e_c_t_s _b_e_t_w_e_e_n _d_i_f_f_e_r_e_n_t _t_y_p_e_s

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

     These functions transform data from one classtype into another, or
     pack simple processes such as compute the profiles needed for one
     annotations package.

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

     as.GOTerms.frame(myGOTermsList, na.rm=TRUE)
     as.GOTerms.list(genelist, probeType, orgPackage=NULL, anotPkg=NULL, onto="any", na.rm=FALSE)
     BioCpack2EntrezIDS(anotPkg, na.rm=FALSE)
     BioCpack2Profiles(anotPkg, orgPackage, level=2, na.rm=FALSE, expanded=FALSE)
     BioCprobes2Entrez(probeslist , anotPkg, na.rm=TRUE)
     GOTermsFrame2GOTermsList(myGOTermsFrame, evid=FALSE)

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

myGOTermsList: GOTermsList object to transform

myGOTermsFrame: GOTermsFrame object to transform

genelist: List of genes (Entrez Ids) to transform

    evid: Type of evidence supporting the selected GO Terms

   na.rm: Flag indicating if those ids returning NA must be removed
          from the output

probeType: Type of probes to transform into Entrez Ids

probeslist: List of probes to transform into Entrez Ids

orgPackage: Name of the organism ('org.Xx.eg.db') annotation package

 anotPkg: Name of the chip annotation package

   level: GO level at which the profile is built

    onto: ontology

expanded: Flag to decide if an expanded profile has to be computed

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

     Not yet available

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

     Every function returns a transformed object or a list of computed
     profiles

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

     Alex Sanchez

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

     data(CD4Ids)
     myGOTermsList <- GOTermsList(CD4LLids[1:5], orgPkg="org.Hs.eg.db")
     myGOTermsFrame<- as.GOTerms.frame(myGOTermsList, na.rm=TRUE)
     GOTermsFrame2GOTermsList(myGOTermsFrame, evid=FALSE)

