GeneIdentifierType         package:GSEABase         R Documentation

_G_e_n_e _I_d_e_n_t_i_f_i_e_r _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:

     Gene identifier classes and functions are used to indicate what
     the list of genes in a gene set represents (e.g., Entrez gene
     identifiers are tagged with 'EntrezIdentifier()', Bioconductor
     annotations with 'AnnotationIdentifier()').

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

     NullIdentifier(annotation, ...)
     EnzymeIdentifier(annotation,...)
     GenenameIdentifier(annotation,...)
     RefseqIdentifier(annotation,...)
     SymbolIdentifier(annotation,...)
     UnigeneIdentifier(annotation,...)
     EntrezIdentifier(annotation,...)
     AnnotationIdentifier(annotation, ...)

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

annotation: An optional character string identifying  the Bioconductor
          package from which the annotations are drawn, e.g.,
          hgu95av2, org.Hs.eg.db.

     ...: Additional arguments, usually none.

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

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

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     'GeneIdentifierType' for a description of the classes and methods
     using these objects.

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

     NullIdentifier()

     data(sample.ExpressionSet)
     gs1 <- GeneSet(sample.ExpressionSet[100:109],
                    setName="sample1", setIdentifier="100")
     geneIdType(gs1) # AnnotationIdentifier

     geneIds <- featureNames(sample.ExpressionSet)[100:109]
     gs2 <- GeneSet(geneIds=geneIds,
                    setName="sample1", setIdentifier="101")
     geneIdType(gs2) # NullIdentifier, since no info about genes provided

     ## Convert...
     ai <- AnnotationIdentifier(annotation(sample.ExpressionSet))
     geneIdType(gs2) <- ai
     geneIdType(gs2)
     ## ...or provide more explicit construction
     gs3 <- GeneSet(geneIds=geneIds, type=ai,
                    setName="sample1", setIdentifier="102")

