GeneSetCollection-methods      package:GSEABase      R Documentation

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

     Use 'GeneSetCollection' to construct a collection of gene sets
     from 'GeneSet' arguments, or a list of 'GeneSet's.

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

     GeneSetCollection(object, ..., idType, setType)

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

  object: An argument determining how the gene set collection will be
          created, as described in the methods section.

     ...: Additional arugments for gene set collection construction, as
          described below.

  idType: An argument of class 'GeneIdentifierType', used to indicate
          how the 'geneIds' will be represented.

 setType: An argument of class 'CollectionType', used to indicate how
          the collection is created.

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


      '_s_i_g_n_a_t_u_r_e(_o_b_j_e_c_t = "_G_e_n_e_S_e_t",_i_d_T_y_p_e="_m_i_s_s_i_n_g", _s_e_t_T_y_p_e="_m_i_s_s_i_n_g")'  
          Construct a gene set collection from one or more 'GeneSet'
          arugments.


      '_s_i_g_n_a_t_u_r_e(_o_b_j_e_c_t = "_l_i_s_t", _i_d_T_y_p_e="_m_i_s_s_i_n_g", _s_e_t_T_y_p_e="_m_i_s_s_i_n_g")'  
          Construct a gene set collection from a list of 'GeneSet's.


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          Construct a gene set collection of 'CollectionType' entities
          (e.g., pathways for 'KEGGCollection', protein families for
          'PfamCollection') implied by the map found in
          'annotation(idType)'. If 'setType' is a 'CollectionIdType'
          and 'length(ids(setType))>0', the gene set collection is
          filtered to contain only those sets implied by the ids.


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          Construct a gene set collection of 'CollectionType' entities
          (e.g., pathways for 'KEGGCollection', protein families for
          'PfamCollection') implied by the map found in
          'annotation(idType)'. Use only those identifiers in 'object'.
          If 'setType' is a 'CollectionIdType' and
          'length(ids(setType))>0', the gene set collection is filtered
          to contain only those sets implied by the ids.


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          Construct a gene set collection using the 'annotation' and
          'featureNames' of 'object' to identify elements for 
          'CollectionType' gene sets (e.g., pathways for
          'KEGGCollection', protein families for 'PfamCollection')
          implied by 'object'. The gene set collection contains only
          those 'AnnotationIdentifiers' found in
          'featureNames(object)'; if 'setType' is a 'CollectionIdType'
          and 'length(ids(setType))>0', the gene set collection is
          further filtered to contain only those sets implied by the
          ids.


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          Construct a gene set collection using the 'annotation' and
          'featureNames' of 'object' to identify  'GO' pathways implied
          by 'object'. The map between 'featureNames' and 'GO' pathway
          identifiers is derived from the 'GO2PROBE' table of the
          annotation package of 'object'. The gene set collection
          contains only those 'AnnotationIdentifiers' found in
          'featureNames(object)'. The 'evidenceCode' of 'GOCollection'
          can be used to restrict the pathways seleted to those with
          matching evidence codes.


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          Construct a gene set collection containing all GO pathways
          referenced in the annotation package of 'idType'. See the
          'signature(object="ExpressionSet", idType="missing",
          setType="GOCollection")' method for details.


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

     'GeneSetCollection'

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

     gs1 <- GeneSet(setName="set1", setIdentifier="101")
     gs2 <- GeneSet(setName="set2", setIdentifier="102")

     ## construct from indivdiual elements...
     gsc <- GeneSetCollection(gs1, gs2)
     ## or from a list
     gsc <- GeneSetCollection(list(gs1, gs2))

     ## set names must be unique
     try(GeneSetCollection(gs1, gs1))

     data(sample.ExpressionSet)
     gsc <- GeneSetCollection(sample.ExpressionSet[200:250],
                              setType = GOCollection())

