clusterAnnotationGO-abp-class   package:goCluster   R Documentation

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

     This class can be used to reorganize the GO annotation from an
     AnnBuilder meta package to make it suitable for the statistical
     analysis.

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

     The class provides a wrapper around the 'prepareGOannotation'
     function. Please read the corresponding documentation for further
     details.

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

     '_m_e_t_a': Object of class '"character"', specifies the AnnBuilder
          meta package which the class will use for the lookup of the
          initial GO IDs.

     '_t_r_u_e_i_d': Object of class '"character"', describes which unique ID
          has been used for building the annotation data package. This
          option is important in case your dataset is annotated with a
          different unique ID. In this case goCluster will have to
          convert the IDs of the dataset into the corresponding
          annotation IDs before removing duplicate entries. 

     '_u_n_i_q_u_e_i_d': Object of class '"character"', this is either a copy
          of the unique id of the parent data object (in case this is
          also the true ID) or a transformed vector according to the
          setting of the true ID. 

     '_o_n_t_o_l_o_g_i_e_s': Object of class '"character"', specifies one or
          several of the three GO ontologies that should be analyzed.

     '_e_v_i_d_e_n_c_e': Object of class '"character"', sets the evidence codes
          that are considered to be acceptable in the analysis.

     Additional slots are described in the documentation of the
     'clusterAnnotation-class' and 'clusterModule-class'.

_E_x_t_e_n_d_s:

     Class '"clusterAnnotation"', directly. Class '"clusterModule"', by
     class '"clusterAnnotation"'.

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

     _c_o_n_f_i_g 'signature(object = "clusterModule")': interactive setup of
          the class. You will be asked to specify the annotation
          package name and the sections of the gene ontology that you
          wish to include in your analysis. In addition unacceptable
          evidence codes can be excluded and the true linking ID can be
          specified.

     _s_e_t_u_p 'signature(object = "clusterModule")': returns the
          configuration of the object as a list. This list can again be
          used for the non-interactive setup of the class. 

     _s_e_t_u_p<- 'signature(object = "clusterModule")': non-interactive
          setup of the class. The options are specified using a list. 

     _e_x_e_c_u_t_e 'signature(object = "clusterModule")': build the GO
          annotation information.

     _r_e_s_e_t 'signature(object = "clusterModule")': remove all annotation
          data that has been retrieved so that the 'execute' function
          can be run again.

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

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

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

     'prepareGOannotation', 'goCluster-class', 'clusterModule-class',
     'clusterAnnotation-class', 'clusterData-class'

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

     ## Predefined setup for goCluster
     data(benomylsetup)

     ## Setup a new goCluster object
     test <- new("goCluster")
     setup(test) <- benomylsetup

     ## We only use the dataset from this object
     data <- test@data

     ## Get the annotation to the dataset
     testAnnotation <- execute(data@anno, test)

