GetStabilityOverlap(GeneSelector)
GetStabilityOverlap()所属R语言包：GeneSelector
Stability measures for gene lists
基因列表的稳定措施
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The similarity of two ordered genelists is assessed by counting the size of the intersection ('overlap') for each position in the list and by computing a weighted cumulative sum of the number of overlaps up to a position in the list ('overlap score'), as suggested by Yang et al. (2006) and Lottaz et al. (2006).
两个有序genelists的相似性进行评估计数为每个列表中的位置，大小路口（重叠），并通过计算加权数列表中的位置重叠的累计总和（重叠得分），由杨等人的建议。 （2006年）和Lottaz等。 （2006年）。
用法----------Usage----------
GetStabilityOverlap(RR, scheme = c("original", "pairwise"), decay = c("linear", "quadratic", "exponential"),
alpha = 1, ...)
参数----------Arguments----------
参数：RR
An object of class RepeatedRanking
一个对象的类RepeatedRanking
参数：scheme
If scheme = "original", a reference list is compared with alternative lists. If scheme = "pairwise", all possible pairs of lists are compared. The latter is normally used in the absence of a reference list, e.g. if the agreement of different ranking procedures is of interest.
如果scheme = "original"，参考名单相比，备选名单。如果scheme = "pairwise"，列出了所有可能的对比。后者通常用来在参考列表的情况下，如如果协议是不同的排名程序的兴趣。
参数：decay
Argument controlling the weight decay of the weights necessary for the computation of the overlap score. If decay="linear", then we have weight 1/l for list position l, if decay="quadratic", then the weight is 1/l^2 and if decay="exponential", then the weight is exp(-alpha*l) where alpha is a tuning parameter, specified via the argument alpha. Weights are used only for the overlap score, not for the intersection count.
参数控制的重叠得分计算所必需的权重衰变。如果decay="linear"的，那么我们有重量1/l列表中的位置l如果decay="quadratic"，然后重1/l^2如果decay="exponential"，然后重量是exp(-alpha*l)alpha是一个调整参数，通过参数alpha指定。只有使用权重重叠得分，而不是交点计数。
参数：alpha
s. decay.
第decay。
参数：...
Currently unused argument.
目前未使用的参数。
值----------Value----------
An object of class StabilityOverlap
一个类StabilityOverlap的对象
注意----------Note----------
作者（S）----------Author(s)----------
Martin Slawski <br>
Anne-Laure Boulesteix
参考文献----------References----------
Assessing stability of gene selection in microarray data analysis. BMC Bioinformatics 7, 50
Similarities of ordered gene lists. Journal of Bioinformatics and Computational Biology 4, 693-708
OrderedList - a Bioconductor package for detecting similarity in ordered gene lists.
参见----------See Also----------
RepeatRanking
RepeatRanking
举例----------Examples----------
## Load toy gene expression data[＃加载玩具基因表达数据]
data(toydata)
### class labels[＃＃类的标签]
yy <- toydata[1,]
### gene expression[＃＃基因表达]
xx <- toydata[-1,]
### get ranking [＃获得排名]
ordT <- RankingTstat(xx, yy, type="unpaired")
### Generate Leave-One-Out[＃生成留出]
loo <- GenerateFoldMatrix(y = yy, k=1)
### Repeat Ranking with t-statistic[＃重复t-统计排名]
loor_ordT <- RepeatRanking(ordT, loo)
### assess stability[＃评估稳定]
stab_ov_ordT <- GetStabilityOverlap(loor_ordT, scheme = "original", decay="linear")
### for a short summary[＃一个简短的摘要]
summary(stab_ov_ordT, measure = "intersection", display = "all", position = 10)
### for a graphical display[图形显示＃]
plot(stab_ov_ordT)
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 19:02:51
