prepareCHRannotation        package:goCluster        R Documentation

_A _f_u_n_c_t_i_o_n _t_o _p_r_e_p_a_r_e _t_h_e _g_e_n_e _l_o_c_a_l_i_z_a_t_i_o_n _f_o_r _s_u_b_s_e_q_u_e_n_t
_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 the chromosome they can be found on.

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

     prepareCHRannotation(uniqueID, annBuilderPkg, chromosomes = NULL, 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. 

chromosomes: The output is restricted to genes lying on these
          chromosomes. 

  trueID: The true ID specifies the type of ID that the chromosome
          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 class retrieves information about the chromosome each gene
     lies on from a given AnnBuilder annotation package and converts
     that information into a format useful for the subsequent analysis.
     The class removes all genes not present in the in the dataset,
     eliminates any duplicate entries (respecting the true ID if
     specified) and can remove any chromosomes that should not be
     included into analysis.

_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 the
          chromosome they lie on. 

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

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

     'clusterAnnotationChromosome-abp-class'

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

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

