run.crossvalidation(gene2pathway)
run.crossvalidation()所属R语言包：gene2pathway
Assessment of Prediction Performance via Cross-validation
通过交叉验证预测绩效评估
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Evaluate the prediction performance of a gene2pathway model via a repeated cross-validation scheme.
通过反复交叉验证计划评估的一个gene2pathway模型的预测性能。
用法----------Usage----------
run.crossvalidation(nfolds=10, repeats=10, stratified=TRUE, signaltrans.only=FALSE, minnmap=ifelse(signaltrans.only, 15, 30), nbag=11, level1Only="Metabolism", level2Only="Genetic Information Processing", organism="hsa", gene2Domains=NULL, seed=1234, mc.cores=8, DIR=".")
参数----------Arguments----------
参数：nfolds
number of cross-validation folds
数量褶皱的交叉验证
参数：repeats
number of repeats of the cross-validation procedure
数重复交叉验证程序
参数：stratified
Ensure that during bagging each class is represented
确保在套袋每一类的代表，
参数：signaltrans.only
do cross-validation for model predicting pathway components of signaling pathways
做交叉验证模型预测信号通路的通路元件
参数：minnmap
prune hierarchy branches with < minnmap mapping genes
<minnmap映射基因修剪层次分行
参数：nbag
number of models to average over
平均模型
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：seed
seed value for random number generator: influences splitting of data into training and test
随机数发生器种子值：影响到训练和测试数据的分裂
参数：DIR
directory where to save diagnostic plots
目录保存诊断图
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 gene2pathway model is trained and tested within a repeated cross-validation scheme. The method produces boxplots (saved as PDFs in the directory passed in the DIR argument) of the accuracy (1 - loss), sensitivity, specificity and F1 values summarized over all pathways. Additionally it produces separate boxplots of F1-values for all pathways in the top KEGG hierarchy level, at the 2nd KEGG hierarchy level and for all pathways individually.
一个gene2pathway模型重复交叉验证计划内的培训和测试。该方法生产的盒状图（保存为PDF文件在DIR参数传递目录）（1 - 损耗）精度，灵敏度，特异性和F1值的所有途径，总结。此外，它产生KEGG层次水平的途径，在第二KEGG层级，并为单独所有途径F1-值独立的盒状图。
值----------Value----------
参数：cv
a matrix of nfolds*repeats rows and as many columns as labels with predictions of the model
一个矩阵模型预测的标签nfolds *重复行和多列
参数：groups
used groups in the cross-validation procedure
在交叉验证过程中使用的组
参数：used_domains
used InterPro domains by the prediction model
InterPro的域所使用的预测模型
参数：evaluation
a list with average loss, sensitivity, specificity and F1-value for each pathway
每个通路的平均损失，敏感性，特异性和F1值列表
作者（S）----------Author(s)----------
Holger Froehlich
参见----------See Also----------
retrain, gene2pathway
retrain，gene2pathway
举例----------Examples----------
## Not run: [＃无法运行：]
run.crossvalidation(signaltrans.only=T, repeats=1, nfolds=2)
## 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 18:35:43
