prepareGOannotation        package:goCluster        R Documentation

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_s_t_a_t_i_s_t_i_c_a_l _a_n_a_l_y_s_i_s

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

     This function builds an association table between a given list of
     genes and their corresponding gene ontology annotations.

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

     prepareGOannotation(uniqueID,
     annBuilderPkg,
     ontologies = ONTOLOGIES,
     evidence = EVIDENCECODES,
     trueID = NULL)

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

uniqueID: The unique ID that should be associated with the gene
          ontology annotation. 

annBuilderPkg: The AnnBuilder package that provides the basis for
          retrieving the annotation information. 

ontologies: The ontologies that should be used. This has to be a
          character vector that contains one or more of the strings
          "MF", "BP", and/or "CC". 

evidence: This character vector should contain the abbreviations for
          acceptable evidence codes. Please see the variable
          EVIDENCECODES for possible choices. The complete vector with
          all evidence codes is the default for the function. 

  trueID: The true ID specifies the type of ID that the gene ontology
          information has been linked to (e.g. Locus Link). If this ID
          differs from the the type of 'uniqueID' this has to be
          specified so that the IDs are converted accordingly. The
          option needs to match the name of the AnnBuilder package
          environment (without the prefix) that provides the conversion
          information. 

_D_e_t_a_i_l_s:

     The gene ontology is organized as a hierarchical tree of terms
     with a parent-child relationship. By associating a gene with a
     term of this ontology the gene is implicitely linked with all
     parents of the term. In order to render the annotation of two gene
     lists comparable it is important to take this relationship into
     account.

     The 'prepareGOannotation' function assembles a complete list of
     gene <-> ontology associations based on the initial, reduced
     annotation. Duplicate genes are removed from the resulting table.
     This removal should be based on the identifiers the gene ontology
     information is linked to (e.g. Lokus Link) and it is possible to
     specify this central ID by setting the 'trueid' option.

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

     A composite list of the (possibly converted) unique ID and the
     association table.

annotations : The association table linking the genes with gene
          ontology terms. Each gene can be linked to multiple GO
          entries and vice versa. 

uniqueid : Either a copy of the original unique identifiers or a
          converted copy that matches the original vector in length but
          specifies the new gene ID for each gene. 

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

     Gunnar Wrobel, <URL: http://www.gunnarwrobel.de>.

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

     'clusterAnnotationGO-abp-class'

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

     prepareGOannotation(c("YGL213C", "YGL215W", "YGL216W", "YGL218W",
     "YGL219C", "YGL220W", "YGL221C", "YGL222C", "YGL223C", "YGL224C",
     "YGL225W"), "YEAST")

