GOTermsList            package:goProfiles            R Documentation

_F_u_n_c_t_i_o_n_s _t_o _c_r_e_a_t_e _a_n_d _m_a_n_a_g_e _l_i_s_t_s _o_f _G_O _t_e_r_m_s _a_s_s_o_c_i_a_t_e_d _w_i_t_h _a _v_e_c_t_o_r _o_f '_E_n_t_r_e_z' _i_d_e_n_t_i_f_i_e_r_s

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

     These functions prepare data to be processed by the 'basicProfile'
     function. To create a profile a set of GOterms belonging to one or
     more ontologies is needed The terms belonging to each gene must be
     given separately so that they can be counted. This function
     queries the environment 'GOENTREZID2GO' with the vector of Entrez
     terms and formats the output into a list whose components -one per
     Entrez term- contain the most specific GO identifiers associated
     with this term.

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

     GOTermsList(LLids, onto = "any", evid = "any", na.rm = FALSE, orgPkg )
     getAncestorsLst(GOtermslist, onto, unique.ancestor=TRUE, na.rm=TRUE, combine=TRUE)
     getGOLevel(onto, level)

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

   LLids: Character vector of 'Entrez' (formerly 'Locuslink'
          identifiers)

    onto: ontology to be queried using the genes list

    evid: type of evidence supporting the selected GO Terms

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

  orgPkg: Organism annotation package ('org.Xx.eg.db') required to
          obtain the GO terms associated with the Entrez identifiers

GOtermslist: List produced by a call to function 'GOTermsList'

unique.ancestor: Flag to remove repeated ancestor identifiers

 combine: Flag to combine ancestors

   level: GO level at which the profile is built

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

     During the call to this function there may appear  two types of
     NAs.

     By one side if a name is not mapped in LocusLink this yields an NA
     that must be eliminated because nothing can be found through LL
     about this name

     By another side if a gene is identified in LL but yields NA it
     seems to mean that it is not mapped in the GO

     This may be eliminated but it may be worth the pity to keep track
     of them and to put these terms in an 'Seemingly unnanotated'
     category. In the case that its number was very high it migt
     suggest reviewing the list or reconsidering the results.

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

     A list whose components -one per Entrez term- are character
     vectors with the most specific GO identifiers associated with this
     term

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

     Alex Sanchez

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

     'getAncestorsLst'

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

     #data(CD4Ids)
     #simpleLLids<- as.character(c(2189,5575,5569,11)) #1 is not a Locuslink identifier
     #simpleGOlist<- GOTermsList (simpleLLids, orgPkg="org.Hs.eg.db")
     #print(simpleGOlist.CC<-GOTermsList (simpleLLids,"CC", orgPkg="org.Hs.eg.db"))
     #print(simpleGOlist.IEA<-GOTermsList (simpleLLids,evid="IEA",na.rm=TRUE, orgPkg="org.Hs.eg.db"))

