OBOCollection-class         package:GSEABase         R Documentation

_C_l_a_s_s "_O_B_O_C_o_l_l_e_c_t_i_o_n"

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

     'OBOCollection' extends the 'GOCollection' class, and is usually
     constructed from a file formated following the OBO file format.
     See 'CollectionType' for general use of collections with gene
     sets.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects are instantiated with calls to 'OBOCollection' or
     'getOBOCollection'.

_S_l_o_t_s:

     'OBOCollection' extends 'GOCollection' and 'OBOCollection' has the
     following additional slots (these slots are NOT meant to be
     manipulated directly by the user):

     '._s_t_a_n_z_a': A 'data.frame' representing the stanzas present in an
          OBO file. Row names of the data frame are unique stanza
          identifiers. The 'value' column contains the stanza name
          (e.g., Term, i.e., the stanza name associated with a GO
          identifier).

     '._s_u_b_s_e_t' A 'data.frame' representing (optional) subsets defined
          in the collection. Subsets are defined in the header of an
          OBO file with a subsetdef tag. Row names of the data frame
          are the subsetdef names; the 'value' column contains the
          subset definition.

     '._k_v' A 'data.frame' representing key-value pairs in the OBO
          source file. The row names of the data frame correspond to
          lines in the OBO file. The 'stanza_id' column indexes the row
          of '.stanza' describing the stanza in which the key-value
          pair occured. The remaining columns ('key', 'value') contain
          the parsed key and value.

_M_e_t_h_o_d_s:

     'OBOCollection' has the following methods, in addition to those
     inherited from 'GOCollection'.

     These methods list and select subsets of 'OBOCollection':

     _s_u_b_s_e_t_s 'signature(object="OBOCollection", display="named")':
          return a character vector of subsets present in 'object'.
          Valid values for 'display' are \sQuote(named) (a named
          character vector, with names equal to the names of the
          subsets and values the descriptions), full (a character
          vector of name and description, with each pair formated into
          a single entry as name (description)), key (subset
          names), or value (subset descriptions).

     [ 'signature(object="OBOCollection", i="character", j="missing",
          ...)': return an 'OBOCollection' by selecting just those
          subsets whose name matches the string(s) in 'i'. This method
          calls the '[,GOCollection' method so, e.g., 'evidenceCode'
          can be used to restricts which evidence codes the collection
          will identify.

     These methods coerce to and from 'OBOCollection':

     _a_s 'signature(object="OBOCollection", "graphNEL")': create a
          directed graph with nodes generated from 'ids(object)' and
          edges from 'is_a' relations of 'object'.

     _a_s 'signature(object="graphNEL", "OBOCollection")': create an
          'OBOCollection' with 'ids' from the graph nodes, and edges
          from 'inNodes(object)'.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     <URL: http://www.geneontology.org> for details of the OBO format.

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

     'OBOCollection' constructor;  'CollectionType' classes.

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

     fl <- system.file("extdata", "goslim_plant.obo", package="GSEABase")
     obo <- getOBOCollection(fl)
     obo
     subsets(obo)
     obo["goslim_plant", evidenceCode="TAS"]
     g <- as(obo["goslim_goa"], "graphNEL")
     if (interactive() && require("Rgraphviz")) {
         plot(g)
     }

