Annotations            package:FunCluster            R Documentation

_F_u_n_c_t_i_o_n_a_l _P_r_o_f_i_l_i_n_g _o_f _M_i_c_r_o_a_r_r_a_y _R_N_A _E_x_p_r_e_s_s_i_o_n _D_a_t_a

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

     This routine belongs to the package FunCluster and performs an
     automated extraction  and update of the Gene Ontology & KEGG
     annotations which are needed for FunCluster analysis.

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

               annotations(date.annot = "")
               

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

date.annot: allows to specify the GO release to be used for annotations
          update. It has no effect on KEGG annotations.

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

     For details concerning FunCluster please see FunCluster help or
     man page 'help(FunCluster)'. The "Annotations" routine is allowing
     the automated extraction and update of the functional annotations
     from their respective web resources. Under common circumstances
     these routine will provide up-to-date annotations, stored into
     environmental variables and directly formatted for FunCluster use.
     Some errors may be seen when using this routine, related to the
     availability of GO annotations for the current month. In case of
     extraction errors, explained most usually by a delay in updating
     GO web servers, the date of the GO release to be used can be
     expressly indicated through the parameter 'annot.date' (see
     example below). The transcript identification system used for
     FunCluster analysis is EntrezGene GeneID's. Please see more
     details on this choice within the JBCB paper.

     Important note for Microsoft Windows users: in order to use this
     routine you will need additional software for handling TAR and
     GZIP archives. Such software is available for Windows under the 
     GNU license.

     For TAR packages you can go to: 
      <URL: http://gnuwin32.sourceforge.net/packages/tar.htm>.  Please
     do not forget to place the TAR executable and its dependencies
     (DLL's)  somewhere into the PATH (like "C:/Windows" for example).
     For GZIP you can go to: 
      <URL: http://gnuwin32.sourceforge.net/packages/gzip.htm>. The
     same observation as for the TAR executables and dependencies
     applies also here.

_N_o_t_e:

     This package is related to a paper submitted to the Journal of
     Bioinformatics and Computational Biology:  Henegar C, Cancello R,
     Rome S, Vidal H, Clement K, Zucker JD. Clustering biological
     annotations and  gene expression data to identify putatively
     co-regulated biological processes.

_R_e_f_e_r_e_n_c_e_s:

     1. Henegar C, Cancello R, Rome S, Vidal H, Clement K, Zucker JD.
     Clustering biological annotations and gene  expression data to
     identify putatively co-regulated biological processes. J Bioinform
     Comput Biol. 2006 Aug; 4(4) (in press).

     2. Cancello R, Henegar C, Viguerie N, Taleb S, Poitou C, Rouault
     C, Coupaye M, Pelloux V, Hugol D, Bouillot  JL, Bouloumie A,
     Barbatelli G, Cinti S, Svensson PA, Barsh GS, Zucker JD, Basdevant
     A, Langin D, Clement K. Reduction of macrophage infiltration and
     chemoattractant gene expression changes in  white adipose tissue
     of morbidly obese subjects after surgery-induced weight loss. 
     Diabetes 2005; 54(8):2277-86.

     3. FunCluster website: <URL:
     http://corneliu.henegar.info/FunCluster.htm>

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

     'FunCluster'.

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

               ## Not run: 
               ## the following example forces the use of a previous GO release 
               (e.g. January 2006) for updating annotations;
               KEGG annotations are not affected by this parameter.
               annotations(date.annot = "200601")
               
     ## End(Not run)

