computeRunningMedians(Ringo)
computeRunningMedians()所属R语言包：Ringo
Function to compute running medians on a tiling expression set
函数来计算运行中位数上一个平铺表达集
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function to compute running medians (or other quantiles) on a tiling expression set.
函数来计算上平铺表达集运行中位数（或其他位数）。
用法----------Usage----------
computeRunningMedians(xSet, probeAnno, modColumn = "Cy5",
allChr, winHalfSize = 400, min.probes = 5, quant = 0.5,
combineReplicates = FALSE, nameSuffix = ".sm", checkUnique=TRUE,
uniqueCodes=c(0), verbose = TRUE)
参数----------Arguments----------
参数：xSet
Object of class ExpressionSet holding the normalized probe intensity data
对象类ExpressionSet控股归探针强度数据
参数：probeAnno
Environment holding the genomic positions of probes in the ExpressionSet
环境在ExpressionSet举行探针基因的位置
参数：modColumn
Column of the ExpressionSet's phenoData holding the samples' difference of interest
列的ExpressionSetphenoData样品息差
参数：allChr
Character vector of all chromosomes in genome; if not specified (defaul) all chromosomes annotated in the supplied probeAnno are used.
（默认情况下将）如果没有指定，所有染色体上注明在所提供的probeAnno用于基因组中的所有染色体的特征向量。
参数：winHalfSize
Half the size of the window centered at a probe position, in which all other probes contribute to the calculation of the median.
在探针的位置，在所有其他探测器的贡献，以中位数计算为中心的窗口的一半大小。
参数：min.probes
integer; if less probes are in the sliding window, NA instead of the median is returned. This meant to avoid to computing non-meaningful medians. If unwanted, set this to 1 or less
整数;如果少探针在滑动窗口，而不是中位数NA是返回。这意味着，以避免非有意义的中位数计算。如果不需要，设置此量小于或等于1
参数：quant
numeric; which quantile to use for the smoothing. The default 0.5 means compute the median over the values in the sliding window.
数值;位数的平滑使用。默认0.5意味着在滑动窗口的值，计算中位数。
参数：combineReplicates
logical; should the median not be computed over individual samples in the ExpressionSet, but should samples be combined according to the column modColumn of the phenoData. The median is then computed across all probe levels and samples of the same type in the window. The resulting ExpressionSet has so many columns as are there different entries in the column modColumn
逻辑;中位数计算，超过个别样品在ExpressionSet样品，但应根据列modColumnphenoData结合。所有探针的水平和在窗口中的相同类型的样本，然后计算中位数。所以产生ExpressionSet已多列，有不同的条目列modColumn
参数：nameSuffix
character; suffix attached to the sample labels of the supplied ExpressionSet xSet for the sample names of the resulting ExpressionSet.
字符;后缀的提供的ExpressionSet的样品标签xSet样品名称产生ExpressionSet的。
参数：checkUnique
logical; indicates whether the uniqueness indicator of probe matches from the probeAnno environment should be used.
逻辑;指示是否应使用的探针匹配从probeAnno环境的独特性指标。
参数：uniqueCodes
numeric; which numeric codes in the chromosome-wise match-uniqueness elements of the probeAnno environment indicate uniqueness?
数字;染色体方面的比赛唯一的probeAnno环境的元素的数字代码表示独特性？
参数：verbose
logical; detailed progress output to STDOUT?
逻辑;详细的进度输出到STDOUT？
值----------Value----------
An object of class ExpressionSet, holding smoothed intensity values for the probes of the supplied ExpressionSet. The number of results samples is either the number of levels in the supplied modColumn of the supplied ExpressionSet's phenoData if combineReplicates is set to TRUE or equal to the number of samples in the supplied ExpressionSet xSet otherwise.
一个类的对象ExpressionSet，控股为提供ExpressionSet探针平滑的强度值。结果样品的数量，要么是水平所提供的modColumn如果combineReplicates设置为TRUE或等于样品提供ExpressionSet的数量xSet，提供的ExpressionSet的phenoData否则。
作者（S）----------Author(s)----------
Joern Toedling
参见----------See Also----------
ExpressionSet,
ExpressionSet
举例----------Examples----------
exDir <- system.file("exData",package="Ringo")
load(file.path(exDir,"exampleProbeAnno.rda"))
load(file.path(exDir,"exampleX.rda"))
smoothX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno,
winHalfSize = 400)
combX <- combine(exampleX, smoothX)
if (interactive()){
grid.newpage()
plot(combX, exProbeAnno, chrom="9", xlim=c(34318000,34321000),
ylim=c(-2,4), gff=exGFF)
}
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 2012-2-26 12:56:59
