retrain.signaltrans       package:gene2pathway       R Documentation

_R_e_t_r_a_i_n _c_l_a_s_s_i_f_i_c_a_t_i_o_n _m_o_d_e_l _f_o_r _s_i_g_n_a_l_i_n_g _p_a_t_h_w_a_y_s

_D_e_s_c_r_i_p_t_i_o_n:

     Retrains the hierarchical classification model for signaling
     pathway components. This way new information from InterPro and
     KEGG databases can be incorporated to give better predictions.
     Retraining should be done on a regular basis from time to time.

_U_s_a_g_e:

     retrain.signaltrans(minnmap=10, organism="hsa", gene2Domains=NULL, remove.duplicates=FALSE, use.bagging=TRUE, nbag=11)

_A_r_g_u_m_e_n_t_s:

 minnmap: prune hierarchy branches with < minnmap mapping genes

organism: KEGG letter code describing an organism.  Please refer to
          <URL:http://www.genome.jp/kegg-bin/create_kegg_menu> for a
          complete list of organisms (and their letter codes) supported
          by KEGG.

gene2Domains: By default associations between genes and InterPro
          domains are retrieved via biomaRt from Ensembl.
          Alternatively, the user can provide its own mapping of genes
          to InterPro domains in form of a list here (see details).

remove.duplicates: remove genes having the same InterPro domains prior
          training 

use.bagging: use bagging 

    nbag: number of models to average over

_D_e_t_a_i_l_s:

     A hierarchical classification model based on SVMs and a ranking
     perceptron algorithm is trained. This model is usually
     additionally bagged to improve prediction qualitiy. The method
     produces a "classificationModelSignalTrans_[organism].rda" (e.g.
     "classificationModelSignalTrans_hsa.rda") file, which should be
     stored in the package data directory. Once a new model has been
     trained, the complete package should be reloaded.

     The current version of the KEGG hierarchy is always retrieved
     directly from KEGG via FTP. Labels for the training set are
     obtained via the function 'getComponents', which uses the KEGG
     SOAP service. By default associations between genes and InterPro
     domains are retrieved automatically via biomaRt from Ensembl.
     Please refer to <URL:http://www.ebi.ac.uk/ensembl/> for a list of
     organisms supported by Ensembl. Alternatively to using Ensembl and
     biomaRt, the user can provide its own mapping of genes to InterPro
     domains in form of a list. This especially allows for using
     organisms, which are supported by KEGG, but not by Ensembl so far.
     The list has the form genes -> InterPro domains, and each list
     entry is named by the Entrez gene ID of the corresponding gene.
     This is, because KEGG uses Entrez gene IDs for the mapping genes
     -> KEGG pathways.

_V_a_l_u_e:

     The model structure. See 'classificationModelSignalTrans' for
     details.

_A_u_t_h_o_r(_s):

     Holger Froehlich

_S_e_e _A_l_s_o:

     'gene2pathway.signaltrans', 'classificationModelSignalTrans'

_E_x_a_m_p_l_e_s:

     ## Not run: 
             retrain.signaltrans() # retrain classification model for signal transduction pathways for human
     ## End(Not run)

