geneRegionScan(GeneRegionScan)
geneRegionScan()所属R语言包：GeneRegionScan
Gene Region Scan
基因区域扫描
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The top-level wrapper function that outputs as much data as possible, concerning one or a few genes. Refer to the functions plotCoexpression and plotOnGene for further explanation of each part of the plot.
顶级的包装函数，输出尽可能多的数据，涉及一个或几个基因。参考职能plotCoexpression和plotOnGene进一步解释每一个图的一部分。
用法----------Usage----------
geneRegionScan(object, gene, genomicData=NULL, probeData=NULL, label=NULL, genename=NULL, summaryType="median", ylim=NULL, testType=NULL,forcePValue=FALSE,verbose=TRUE,cutoff=0.2, directions="all",correlationCutoff=0.3, probeLevelInfo=c("probeid"))
参数----------Arguments----------
参数：object
A ProbeLevelSet object or a regular ExpressionSet object (in which case a probeData argument is required). See getLocalProbeIntensities and related functions on how to create a ProbeLevelSet.
一个ProbeLevelSet对象或定期ExpressionSet对象（在这种情况下probeData参数是必需的）。如何创建一个ProbeLevelSet getLocalProbeIntensities和相关职能。
参数：gene
A number of gene sequences as DNAString, list of DNAString objects, character-vectors or readFASTA outputs.
一个基因序列作为DNAString，列表DNAString对象，字符矢量或readFASTA输出的数量。
参数：genomicData
Optional. If only one gene is specified this can be of the same form as given in exonStructure. If more than one gene is given, it must be a list, containing of one of these forms of the argument for each of the genes, in the same order.
可选的。如果只指定了一个基因可以是相同的形式，在exonStructure。如果一个以上的基因，它必须是一个列表，包含每个基因的争论这些形式之一，在相同的顺序。
参数：probeData
Optional if a ProbeLevelSet is submitted as object argument. Otherwise, it must be a data frame with rownames corresponding to the featureNames of the ExpressionSet and a column named "sequence" with the probe sequences as character strings
可选如果提交对象参数ProbeLevelSet。否则，它必须是一个相应的ExpressionSet的featureNames和探针序列作为字符串名为“序列”列rownames数据框
参数：label
An optional character string specifying a column name in the pData of the object. If this argument is given, the gene plot will be colour coded based on the different groups (factors) in the pData entry. If a summaryType other than 'dots' is selected the summarisation is done stratified by the different groups in the pData.
一个可选的字符串对象的pData所指定的列名。如果这种说法，基因图将根据不同的群体，在PDATA项（因素）的颜色编码。如果选择“点”以外summaryType的summarisation完成在pData所不同群体分层。
参数：genename
Optional character string specifying a gene name to include in the plot. If not included and a FASTA sequence is given, it will default to the name in the FASTA sequence. Otherwise it will default to 'Unknown genename'.
可选的字符串指定一个基因的名字，包括图。如果不包含，并给出一个FASTA序列，它会默认为FASTA格式的序列的名称。否则，它会默认为未知genename“。
参数：summaryType
Character string specifying one of the following summary methods: 'median', 'mean', 'quartiles' or 'dots' (i.e. no summary). Specifies how all the sample values or all the samples values in a group if 'label' is given, should be summarised. Defaults to 'median'.
字符串，指定以下的简易方法之一：“中位数”，“意味着”，“四分”或“点”（即无摘要）。指定所有样本值或一组中的所有样本值，如果给出标签，应该总结。默认为“中位数”。
参数：testType
Optional character string, defining a statistic procedure to identify especially interesting probes. Can be either 'linear model', 'students' or 'wilcoxons'. If given, a label must also be specified. In this case the plotStatistics function will be called and probes that are significantly changed between the groups in label at the P-value set in cutoff (see cutoff argument) will be circled.
可选的字符串，定义一个统计程序，以确定特别有趣的探针。可无论是“线性模型”，“学生”或“wilcoxons”。如果给出一个标签还必须指定。在这种情况下的plotStatistics函数将被调用，将盘旋在标签的群体之间有显着改变，在截止一套P值（见截止参数）的探针。
参数：forcePValue
Logical. Is used if the testType argument is used. If TRUE all significantly changed probes have P-value given on the plot. If FALSE, only plots with less than 10 significant probes write P-values. Plots can become very cluttered with data if set to TRUE
逻辑。用于用于，如果testType参数。如果真探针均显着改变，有图给予的P值。如果为FALSE，只用不到10显著探针图写出P值。图可以成为非常杂乱的数据，如果设置为TRUE
参数：verbose
TRUE or FALSE
TRUE或FALSE
参数：cutoff
Integer specifying at what p-value probes should be circled when using the 'testType' variable. Defaults to 0.2. For cutoffs higher than 0.05, all probes with P >0.05 will be circled in grey instead of black.
整数，指定p值探针应盘旋时使用的“testType变量。默认为0.2。比0.05的临界值，P均> 0.05探针将在灰黑色的，而不是盘旋。
参数：directions
A character vector of the matching-directions that should be scanned (which combinations of complementary and reverse). Defaults to "all" which is shorthand for all possible directions, but can take anything from: c("matchForwardSense", "matchForwardAntisense", "matchReverseSense", "matchReverseAntisense")
应扫描（互补和反向组合）的匹配方向的一个特征向量。默认“所有”，这是对所有可能的方向速记，但可以采取任何来自：C（“matchForwardSense”，“matchForwardAntisense”，“matchReverseSense”，“matchReverseAntisense”）
参数：correlationCutoff
A number between 0 and 1. The limit at which Pearson correlation (in absolute values) should not be plotted below. Defaults to 0.5
0和1之间的数字。 Pearson相关系数（绝对值）的限制，不应该被绘制在下面。默认0.5
参数：probeLevelInfo
The information about each probe to include in the plot. Should be a vector of one or more of the following elements: probeid, probesetid, sequence. Default is only probeid.
每个探针的信息，包括在图。应该是一个向量的一个或多个下列元素：probeid，probesetid序列。默认只probeid。
参数：ylim
Label of Y-axis as in default plots
Y轴标签在默认图
Details
详情----------Details----------
This function is a wrapper around plotOnGene and plotCoexpression. The output of plotOnGene is included in the top half of the plot and the output of plotCoexpression will be included in the bottom half of the plot. Refer to each of these functions for more detailed help.
这功能是围绕plotOnGene和plotCoexpression的包装。的plotOnGene输出包括在该图的上半部分和输出plotCoexpression将包括在该图的下半部。请参阅更详细的帮助这些功能。
In general, this function gives an overview of how intensity values of individual probes on a microarray are in relation to an actual gene or set of genes in a region of the genome.
这个功能在一般情况下，一个芯片上个别探针的强度值如何在实际的基因或基因组的基因组区域的关系，给出了一个概述。
The function has only been tested with up to four genes at the same time. A plot with more genes would probably also be too complicated to interpret with this method. In addition, the alignment of the top and bottom plots also becomes somewhat difficult with more genes. This alignment is also the reason why the function can not export to any device.
函数只被测试了在同一时间到四个基因。与更多的基因图，可能还太复杂，用这种方法来解释。此外，调整顶部和底部的图也变得有点困难更多的基因。这一调整也是函数的原因不能出口到任何设备。
See getLocalProbeIntensities for more info on how to obtain ProbeLevelSets.
查看更多如何获得ProbeLevelSets的信息getLocalProbeIntensities。
值----------Value----------
No value, but plots the local expression levels of each probe found in the submitted sequence of the gene or genes as a function of its location along this sequence on the top half of a pdf-file. On the bottom half of the pdf-file it will plot the pairwise correlations between all probes found in the sequences. The pdf file will be named "report\_" + title
没有价值，但图在提交作为其位置上的PDF文件的上半部分沿此序列功能的基因或基因序列，发现每个探针的地方表达水平。上下半部的PDF文件，它会绘制成对的序列中发现的所有探针之间的相关性。 PDF文件将被命名为“报告\”称号
作者（S）----------Author(s)----------
Lasse Folkersen
参见----------See Also----------
plotCoexpression, plotOnGene, getLocalProbeIntensities
plotCoexpression，plotOnGene，getLocalProbeIntensities
举例----------Examples----------
data(exampleProbeLevelSet)
#simple:[很简单：]
geneRegionScan(exampleProbeLevelSet,mrna)
#more complicated - note that we slice the mrna to simulate comparing two different isoforms[更为复杂 - 注意，我们模拟比较两个不同的亚型的mRNA切片]
gene1<-DNAString(mrna[[1]]$seq)[1:1000]
gene2<-DNAString(mrna[[1]]$seq)[1500:3000]
geneRegionScan(exampleProbeLevelSet, list(gene1,gene2), genomicData=list(genomic,genomic), label="genotype3", summaryType="mean",
testType="linear model", forcePValue=TRUE, cutoff=0.1, directions="all", correlationCutoff=0.6,
probeLevelInfo=c("probeid","sequence"))
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 18:58:21
