findChersOnSmoothed(Ringo)
findChersOnSmoothed()所属R语言包：Ringo
Find ChIP-enriched regions on smoothed ExpressionSet
发现芯片富集区域平滑ExpressionSet
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Given an ExpressionSet of smoothed probe intensities, an environment with the mapping of probes to chromosomes, and a vector of thresholds for calling genomic sites enriched, this function finds the 'chers' (ChIP-enriched regions) consisting of enriched genomic positions, with probes mapped to them. 'Adjacent' enriched positions are condensed into a single Cher.
此功能给予ExpressionSet平滑探针强度，环境与染色体探针的映射，并调用丰富的基因网站的向量的阈值，发现“chers（芯片丰富的区域）组成的丰富的基因组位置与探针，映射到它们。 “邻”富硒位置都凝结成一个单一的雪儿。
用法----------Usage----------
findChersOnSmoothed(smoothedX, probeAnno, thresholds, allChr = NULL,
distCutOff = 600, minProbesInRow = 3, cellType = NULL,
antibodyColumn=NULL, checkUnique = TRUE, uniqueCodes = c(0),
verbose = TRUE)
参数----------Arguments----------
参数：smoothedX
Object of class ExpressionSet holding the smoothed probe intensities, e.g. the result of function computeRunningMedians.
对象类ExpressionSet控股平滑探针强度，例如：功能computeRunningMedians的结果。
参数：probeAnno
environment containing the probe to genome mapping
环境包含探针基因组图谱
参数：thresholds
numeric vector of threshold above which smoothed probe intensities are considered to correspond to enriched probes. The vector has to be of length equal the number of samples in smoothedX, with a single threshold for each sample.
上方平滑探针强度阈值的数字矢量被认为是对应丰富探针。矢量的长度等于smoothedX为每个样品的单阈值，样本数。
参数：allChr
character vector of all chromosomes on which enriched regions are sought. Every chromosome here has to have probes mapped to it in the probeAnno environment. By default (NULL) the chromosomeNames of the probeAnno object are used.
所有染色体上丰富的区域寻求的特征向量。这里每一个染色体有probeAnno环境映射到它的探针。默认情况下（NULL）chromosomeNames的probeAnno对象使用。
参数：distCutOff
integer; maximum amount of base pairs at which enriched probes are condensed into one Cher.
整数;碱基对的最高金额，在丰富的探针凝结成一个雪儿。
参数：minProbesInRow
integer; minimum number of enriched probes required for a Cher; see details for further explanation.
整数;最低数量为雪儿需要丰富的探针，看到details作进一步的解释。
参数：cellType
character; name of cell type the data comes from, is either a. of length one indicating the column of pData(smoothedX) that holds the cell type OR b. of length one indicating the common cell type for all samples in the ExpressionSet OR c. of length equal to ncol(smoothedX) specifying the cell type of each sample individually.
字符;单元类型的数据，从名称可以是一个。显示的列的长度为一pData(smoothedX)保存的单元类型或B。长度为一常见的单元类型ExpressionSet或C表明所有样品。长度等于ncol(smoothedX)单独指定每个样品的单元类型。
参数：antibodyColumn
the name or number of the column of the pData(smoothedX) that holds the description of the antibody used for each sample. This information is used to annotate found ChIP-enriched regions accordingly. If NULL (default), the sampleNames of smoothedX are used.
名称或数量的pData(smoothedX)列保存每个样品所使用的抗体的描述。此信息用于相应注解芯片丰富的区域。如果NULL（默认），sampleNamessmoothedX正在使用。
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; extended output to STDOUT?
逻辑扩展输出到STDOUT？
Details
详情----------Details----------
Specifying a minimum number of probes for a Cher (argument minProbesInRow) guarantees that a Cher is supported by a reasonable number of measurements in probe-sparse regions. For example, if there's only one enriched probe within a certain genomic 1kb region and no other probes can been mapped to that region, this single probe does arguably not provide enough evidence for calling this genomic region enriched.
指定最低数量为雪儿（参数minProbesInRow），雪儿合理数量的测量探针稀疏区域的支持，保证了探针。例如，如果只有一个丰富探针一定1kb的基因组区域内，并没有其他的探针可以被映射到该区域的，这个单一探针，可以说没有调用这个丰富的基因组区域提供足够的证据。
值----------Value----------
A list of class cherList, holding objects of class cher that were found on the supplied data.
类cherList，持有类对象的名单cher提供的数据发现。
作者（S）----------Author(s)----------
Joern Toedling
参见----------See Also----------
cherByThreshold,computeRunningMedians,
cherByThreshold，computeRunningMedians
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,
modColumn = "Cy5", allChr = "9", winHalfSize = 400)
chersX <- findChersOnSmoothed(smoothX, probeAnno=exProbeAnno,
thresholds=0.45, allChr="9", distCutOff=600, cellType="human")
if (interactive())
plot(chersX[[1]], smoothX, probeAnno=exProbeAnno, gff=exGFF)
chersX <- relateChers(chersX, exGFF)
as.data.frame.cherList(chersX)
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 12:57:44
