getOBOCollection          package:GSEABase          R Documentation

_R_e_a_d _O_B_O-_s_p_e_c_i_f_i_e_d _G_e_n_e _O_n_t_o_l_o_g_y _C_o_l_l_e_c_t_i_o_n_s

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

     'getOBOCollection' parses a uri (file or internet location)
     encoded following the OBO specification defined by the Gene
     Onotology consortium.

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

     getOBOCollection(uri, evidenceCode="ANY", ...)

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

     uri: A file name or URL containing gene sets encoded following the
          OBO specification.

evidenceCode: A character vector of evidence codes.

     ...: Further arguments passed to the 'OBOCollection' constructor.

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

     'getOBOCollection' returns an 'OBOCollection' of gene sets. The
     gene set is constructed by parsing the file for 'id' tags in
     'TERM' stanzas. The parser does not currently support all features
     of OBO, e.g., the ability to import additional files.

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

     Martin Morgan <mtmrogan@fhcrc.org>

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.geneontology.org>

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

     'OBOCollection', 'OBOCollection'

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

     ## 'fl' could also be a URI
     fl <- system.file("extdata", "goslim_plant.obo", package="GSEABase")
     getOBOCollection(fl) # GeneSetCollection of 2 sets

     ## Not run: 
     ## Download from the internet
     fl <- "http://www.geneontology.org/GO_slims/goslim_plant.obo"
     getOBOCollection(fl, evidenceCode="TAS")
     ## End(Not run)

