clusterAnnotationChromosome-abp-classpackage:goClusterR Documentation

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

     This class can be used to retrieve the chromosome information for
     subsequent use in a 'goCluster'-analysis.

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

     The class provides a wrapper around the 'prepareCHRannotation'
     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 that the class will use for the lookup of
          chromosome information.

     '_t_r_u_e_i_d': Object of class '"character"', describes which id has
          actually been used for the building of the annotation package
          (this is important for some of the AnnBuilder packages that
          use LocusLink as central ID.

     '_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.

     '_c_h_r_o_m_o_s_o_m_e_s': Object of class '"character"', this can be used to
          limit the analysis to specific chromosomes.

     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 chromosomes that you wish to include in
          your analysis. In addition 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
          chromosome 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:

     'prepareCHRannotation', '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

     ## The predefined configuration is set to retrieve the
     ## gene ontology information. We need to exchange this
     ## with chromosome annotation
     anno <- new("clusterAnnotationChromosome-abp")
     setup(anno) <- list(meta = "YEAST",
                         chromosomes = as.character(seq(1:16)),
                         trueid = "")
     data@anno <- anno

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

