CollectionType-class        package:GSEABase        R Documentation

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

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

     These classes provides a way to tag the origin of a 'GeneSet'.
     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'.)

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

     The following classes can tag gene sets; 'GO, KEGG, Chr, Chrloc,
     OMIM, and PMID' collections can be derived from chip or organism
     annotation packages.

     _N_u_l_l_C_o_l_l_e_c_t_i_o_n No formal collection information available.

     _B_r_o_a_d_C_o_l_l_e_c_t_i_o_n Derived from, or destined to be, Broad XML.
          Usually created and written 'getBroadSets', 'toBroadXML'.

     _E_x_p_r_e_s_s_i_o_n_S_e_t_C_o_l_l_e_c_t_i_o_n Derived from 'ExpressionSet'. Usually
          created during a call to 'GeneSet' or 'GeneColorSet'.

     _G_O_C_o_l_l_e_c_t_i_o_n Collection derived using Gene Ontology (GO) terms.

     _K_E_G_G_C_o_l_l_e_c_t_i_o_n Collection derived using KEGG terms.

     _C_h_r_C_o_l_l_e_c_t_i_o_n Collection derived using chromsome locations

     _C_h_r_l_o_c_C_o_l_l_e_c_t_i_o_n Collection derived using chromosome starting
          posistions

     _M_a_p_C_o_l_l_e_c_t_i_o_n Collection derived from cytogenic bands.

     _O_M_I_M_C_o_l_l_e_c_t_i_o_n Collection derived from identifiers in the Online
          Inheritance in Man.

     _P_M_I_D_C_o_l_l_e_c_t_i_o_n Collection derived from PMID identifiers.

     _P_f_a_m_C_o_l_l_e_c_t_i_o_n Collection derived from Pfam identifiers.

     _P_r_o_s_i_t_e_C_o_l_l_e_c_t_i_o_n Collection derived from Prosite identifiers.

     Objects are instantiated with calls to 'CollectionType'
     constructors, with slot names as possible arguments.

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

     'CollectionType' classes ('Null, ExpressionSet') have the slot:

     '_t_y_p_e': Object of class '"ScalarCharacter"' containing the
          character string representation of this 'CollectionType'.

     'CollectionIdType' classes ('KEGG, OMIM, PMID, Chr, Chrloc, Map,
     GO') extend the 'CollectionType' and have the additional slot:

     '_i_d_s': Object of class '"character"' containing a vector of
          character string representations of corresponding
          identifiers, e.g., KEGG or GO terms.

     'GOCollection' extends 'CollectionIdType' and has the additional
     slot:

     '_e_v_i_d_e_n_c_e_C_o_d_e': Object of class '"character"', containing GO
          evidence codes used to construct the gene set.

     'BroadCollection' has slots:

     '_c_a_t_e_g_o_r_y': Object of class '"ScalarCharacter"' containing terms
          from the Broad list of categories, or 'NA'

     '_s_u_b_C_a_t_e_g_o_r_y': Object of class '"ScalarCharacter"' containing
          Broad sub-categories, or 'NA'

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

     'CollectionType' classes have methods:

     _c_o_l_l_e_c_t_i_o_n_T_y_p_e<- 'signature(object = "GeneSet", value =
          "CollectionType")': Replace the 'CollectionType' 

     _c_o_l_l_e_c_t_i_o_n_T_y_p_e 'signature(object = "CollectionType")': Retrieve
          the collection type.

     _s_h_o_w 'signature(object = "CollectionType")': display the
          collection type.

     'CollectionIdType' classes inherit 'CollectionType' methods, and
     have in addition:

     _i_d_s 'signature(object="CollectionIdType")': Retrieve the
          identifiers of the collection type.

     'GOCollection' inherits 'CollectionIdType' methods, and has in
     addition:

     _e_v_i_d_e_n_c_e_C_o_d_e Retrieve the evidence codes of the GO collection.
          Evidence codes are summarize in, e.g., 'GOENTREZID'.

     'BroadCollection' has methods:

     _b_c_C_a_t_e_g_o_r_y Retrieve the 'category' of the Broad collection.

     _b_c_S_u_b_C_a_t_e_g_o_r_y Retrieve the sub-category of the Broad collection.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     'CollectionType' consturctors.

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

     getSubclasses(getClass("CollectionType"))

     ## Create a CollectionType and ask for its type
     collectionType(ExpressionSetCollection())

     ## Not run: 
     ## Read two GeneSets from a Broad XML file into a list, verify that
     ## they are both BroadCollection's. Category / subcategory information
     ## is unique to Broad collections.
     fl <- system.file("extdata", "Broad.xml", package="GSEABase")
     sets <- getBroadSets(fl)
     sapply(sets, collectionType)
     ## End(Not run)

     ## ExpressionSets are tagged with ExpressionSetCollection; there is no
     ## 'category' information.
     data(sample.ExpressionSet)
     gs <- GeneSet(sample.ExpressionSet[100:109],
                   setName="sample.GeneSet", setIdentifier="123")
     collectionType(gs)

     ## GOCollections are created by reference to GO terms and evidenceCodes
     GOCollection("GO:0005488")
     ## requires library(GO); EntrezIdentifers automatically created
     ## Not run: 
     GeneSet(GOCollection(c("GO:0005488", "GO:0019825"),
                          evidenceCode="IDA"))
     ## End(Not run)

