CollectionType           package:GSEABase           R Documentation

_C_o_l_l_e_c_t_i_o_n _T_y_p_e _C_l_a_s_s _C_o_n_s_t_r_u_c_t_o_r_s

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

     These functions construct collection types. Collection types can
     be used in manipulating (e.g., selecting) sets, and can contain
     information specific to particular sets (e.g., 'category' and
     'subcategory' classifications of 'BroadCollection'.)

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

     NullCollection(...)
     ComputedCollection(...)
     ExpressionSetCollection(...)
     ChrCollection(ids,...)
     ChrlocCollection(ids,...)
     KEGGCollection(ids,...)
     MapCollection(ids,...)
     OMIMCollection(ids,...)
     PMIDCollection(ids,...)
     PfamCollection(ids, ...)
     PrositeCollection(ids, ...)
     GOCollection(ids=character(0), evidenceCode="ANY", ontology="ANY", ..., err=FALSE)
     OBOCollection(ids, evidenceCode="ANY", ontology="ANY", ...)
     BroadCollection(category, subCategory=NA, ...)

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

category: (Required) Broad category, one of "c1" (postitional), "c2"
          (curated), "c3" (motif), "c4" (computational), "c5" (GO).

subCategory: (Optional) Sub-category; no controlled vocabulary.

     ids: (Optional) Character vector of identifiers (e.g., GO, KEGG,
          or PMID terms).

evidenceCode: (Optional) Character vector of GO evidence codes to be
          included, or "ANY" (any identifier; the default).  Evidence
          is a property of particular genes, rather than of the
          ontology, so evidenceCode is a convenient way of specifying
          how users of a GOCollection might restrict derived objects
          (as in done during create of a gene set from an expression
          set).

ontology: (Optional) Character vector of GO ontology terms to be
          included, or "ANY" (any identifier; the default). Unlike
          evidence code, ontology membership is enforced when
          GOCollection gene sets are constructed.

     err: (Optional) logical scalar indicating whether non-existent GO
          terms signal an error ('TRUE'), or are silently ignored
          ('FALSE').

     ...: Additional arguments, usually none but see specific
          'linkS4class{CollectionType}' classes  for possibilities.

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

     An object of the same class as the function name, initialized as
     appropriate for the collection.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     'CollectionType',

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

     NullCollection()

     ## NullCollection when no collection type specified
     collectionType(GeneSet())
     collectionType(GeneSet(collectionType=GOCollection()))

     ## fl could be a url
     fl <- system.file("extdata", "Broad.xml", package="GSEABase")
     gs1 <- getBroadSets(fl)[[1]]
     collectionType(gs1) # BroadCollection

     ## new BroadCollection, with different category
     bc <- BroadCollection(category="c2")
     ## change collectionType of gs2
     gs2 <- gs1
     collectionType(gs2) <- NullCollection()

     ## OBOCollection
     fl <- system.file("extdata", "goslim_plant.obo", package="GSEABase")
     getOBOCollection(fl, evidenceCode="TAS") # returns OBOCollection
     OBOCollection(c("GO:0008967", "GO:0015119", "GO:0030372", "GO:0002732",
                     "GO:0048090"))

