retrain {gene2pathway}R Documentation

Retrain classification model

Description

Retrains the hierarchical classification model. 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.

Usage

retrain(minnmap=30, level1Only="01100", level2Only=c("01200"), organism="hsa", gene2Domains=NULL, KEGG.package=FALSE, remove.duplicates=FALSE, use.bagging=TRUE, nbag=11)

Arguments

minnmap prune hierarchy branches with < minnmap mapping genes
level1Only for these hierarchy branches only the first level is used
level2Only for these hierarchy branches only the first and the second levels are used
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).
KEGG.package Instead of retrieving information directly from KEGG, one can use the KEGG.db package instead, which is significantly faster. However, the KEGG.db package only supports a fraction of organisms so far. Please refer to the manual pages of the KEGG.db package for further information. Default: Don't use KEGG.db package
remove.duplicates remove genes having the same InterPro domains prior training. Default: Don't do this
use.bagging use bagging
nbag number of models to average over

Details

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 "classificationModel_[organism].rda" (e.g. "classificationModel_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. 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.

Value

The model structure. See classificationModel for details.

Author(s)

Holger Froehlich

See Also

gene2pathway, classificationModel


[Package gene2pathway version 1.0 Index]