clusterAnnotationLookup-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 provide LocusLink IDs via a lookup
     table. The LocusLink ID's will then be mapped to GO identifiers.

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

     The lookup file must have the common csv format. It must provide a
     header  with the column names and the values are seperated by ",".
     The file may  only have two columns. The first column specifies
     the locus link ID, the second column represents the matching gene
     ID. Please ensure that the  gene ID's do match exactly to the
     rownames in your dataset.

     While this class only links LocusLink with Go it is actually a
     good example of how you can import external data from a lookup
     table into the statistical analysis process of goCluster.

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

     '_l_o_o_k_u_p': Path to the lookup table.

     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 = "clusterAnnotationLookup")':
          interactive setup of the class. You will be asked to specify
          the path of the lookup file.

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

     _e_x_e_c_u_t_e 'signature(object = "clusterAnnotationLookup")': build the
          annotation information to make it suitable for  statistical
          analysis.

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

     _p_r_i_n_t 'signature(object = "clusterAnnotationLookup")': This
          function prints some basic information about the content of
          this object.

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

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

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

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

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

