retrain(gene2pathway)
retrain()所属R语言包：gene2pathway
Retrain classification model
重新训练分类模型
译者：生物统计家园网 机器人LoveR
描述----------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.
再培训的层次分类模型。这种方式从InterPro和KEGG资料库的新信息可以纳入，以提供更好的预测。应做定期不时再培训。
用法----------Usage----------
retrain(minnmap=30, level1Only="Metabolism", level2Only="Genetic Information Processing", organism="hsa", gene2Domains=NULL,remove.duplicates=FALSE, use.bagging=TRUE, nbag=11, mc.cores=8)
参数----------Arguments----------
参数：minnmap
prune hierarchy branches with < minnmap mapping genes
<minnmap映射基因修剪层次分行
参数：level1Only
for these hierarchy branches only the first level is used
只有这些层次分支使用的第一级
参数：level2Only
for these hierarchy branches only the first and the second levels are used
使用这些层次分支，只有第一和第二的水平
参数：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.
KEGG字母代码描述一个有机体。一个生物体KEGG支持（以及他们的字母代码）的完整列表，请参阅<URL:http://www.genome.jp/kegg-bin/create\_kegg\_menu>。
参数：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).
默认情况下，基因和InterPro的域之间的关联是通过从Ensembl的biomaRt检索。另外，用户可以提供自己的基因映射到InterPro的形式在这里列表域（见详情）。
参数：remove.duplicates
remove genes having the same InterPro domains prior training. Default: Don't do this
删除基因具有相同的InterPro的域前培训。默认：不要这样做
参数：use.bagging
use bagging
使用套袋
参数：nbag
number of models to average over
平均模型
参数：mc.cores
number of cores to use for parallelization; requires package 'doMC' to be loaded
要求包“doMC要加载核心并行使用;
Details
详情----------Details----------
A hierarchical classification model based on SVMs and a ranking perceptron algorithm is trained. This model is usually additionally bagged to improve prediction quality. 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 detached and reloaded.
分层分类模型基于支持向量机和排名感知算法进行训练。这种模式通常是加套袋，以提高预测质量。该方法产生一个“classificationModel \ _ [有机体。RDA”（如“classificationModel \ _hsa.rda”）的文件，该文件应存储在包中的数据目录。一旦经过训练的一种新模式，完整的包应该被分离并重新加载。
The KEGG hierarchy is taken from the package keggorthology. 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.
KEGG层次采取从包keggorthology。基因和InterPro的域之间的关联，默认情况下，通过自动检索从Ensembl的biomaRt。请参考Ensembl的支持生物名单，以<URL:http://www.ebi.ac.uk/ensembl/>。 Ensembl的和biomaRt使用或者，用户可以提供自己的基因映射到InterPro的域列表的形式。尤其是允许使用的生物体，这是KEGG支持，但到目前为止，由Ensembl的。列表形式的基因 - > InterPro的域，每个列表项由Entrez基因相应的基因ID命名。
值----------Value----------
The model structure. See classificationModel for details.
模型的结构。看到classificationModel详情。
作者（S）----------Author(s)----------
Holger Froehlich
参见----------See Also----------
gene2pathway, classificationModel
gene2pathway，classificationModel
举例----------Examples----------
## Not run: [＃无法运行：]
retrain(organism="dme") # retrain classification model for drosophila[果蝇的重新训练分类模型]
## End(Not run)[＃结束（不运行）]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-25 18:35:36
