GetStabilityUnion(GeneSelector)
GetStabilityUnion()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 multiple ordered genelists is assessed by counting the size of the union ('union count') for each position in the list. The higher the union count, the less stable are the ordered lists. Similarly to the 'overlap score' of Yang et al. (2006), Lottaz et al. (2006), we compute a weighted average of the union count entitled 'union score' .
计数为每个列表中的位置，大小工会（工会数）评估的多个下令genelists相似。工会计数较高，不太稳定的有序列表。同样的重叠得分，杨等人。 （2006年），Lottaz等。 （2006年），我们计算了题为“联盟得分”工会数量的加权平均。
用法----------Usage----------
GetStabilityUnion(RR, decay = c("linear", "quadratic", "exponential"),
alpha = 1, noinformation = 0,...)
参数----------Arguments----------
参数：RR
An object of class RepeatedRanking
一个对象的类RepeatedRanking
参数：decay
Argument controlling the weight decay of the weights used for the computation of the union 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 union score, not for the union count.
参数控制用于计算联盟得分权重的重量衰变。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。权重仅用于工会得分，不为工会计数。
参数：alpha
s. decay.
第decay。
参数：noinformation
If noinformation is a positive integer, union count and -score in the no-information case are approximated by randomly generating multiple lists and computing scores noinformation times and averaging the results. Note that this procedure can be rather slow, depending on the number and the length of the lists to be compared.
noinformation如果是一个正整数，工会数和得分在没有资料的情况下，通过随机生成多个列表和计算分数noinformation倍，平均的结果近似。请注意，这个过程可以是相当缓慢的，根据名单的数量和长度进行比较。
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----------
Union count and union score are suitably normalized to fall into the unit interval for the sake of better interpretability, with zero corresponding to maximal instability.
计数联盟和联盟得分适当标准化陷入为了更好的解释性单位区间，对应的最大不稳定，零。
Note that this function yields exactly one stability score for multiple lists, as opposed to the pairwise approach in GetStabilityOverlap and GetStabilityDistance.
请注意，此功能会产生多个列表的一个稳定的得分，而不是成对到在GetStabilityOverlap和GetStabilityDistance的方法。
作者（S）----------Author(s)----------
Martin Slawski <br>
Anne-Laure Boulesteix
参考文献----------References----------
Current Opinion in Structural Biology 13, 370-376.
Algebraic stability indicators for ranked lists in molecular profiling. Bioinformatics 24, 258-264
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_union_ordT <- GetStabilityUnion(loor_ordT, decay="linear")
### display the result[＃显示结果]
plot(stab_union_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。
|
发表于 2012-2-25 19:02:59
