plotCoexpression(GeneRegionScan)
plotCoexpression()所属R语言包：GeneRegionScan
Plot Coexpression of probes in a ProbeLevelSet
探针在ProbeLevelSet图的共表达
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function that will investigate all possible pairings in a set of probes, calculate the Pearson correlation coefficient and plot them in a meaningful way
功能，将调查所有可能的配对，在一组探针计算Pearson相关系数，并以有意义的方式绘制
用法----------Usage----------
plotCoexpression(object, gene, probeData=NULL, verbose=TRUE, directions="all", correlationCutoff=0.5,
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, vectors of DNAStrings, character-vectors or readFASTA outputs.
一个号码作为DNAstring基因序列，向量DNAStrings，字符矢量或readFASTA输出的。
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，它必须是一个数据框与相应的ExpressionSet featureNames和探针序列作为字符串名为“序列”列rownames
参数：verbose
TRUE or FALSE
TRUE或FALSE
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。
Details
详情----------Details----------
This function takes a ProbeLevelSet or an ExpressionSet + probeData and the sequence of a gene. It then calculates pairwise Pearson correlation coefficients between all possible combinations of probes. Then it assigns each probe to a location along the length of the gene and plots a relational graph showing which probes has high correlation coefficients. The correlation coefficients are sorted by
这个函数接受一个ProbeLevelSet或ExpressionSet + probeData和基因序列。然后计算成对的皮尔逊相关系数探针之间的所有可能的组合。然后分配给每个探针的位置沿长度的基因，并绘制关系图，显示该探针具有较高的相关系数。相关系数排序
值----------Value----------
No value, but plots a hapmap style plot of correlation values between all probes
没有价值，但图的相关值HapMap的风格之间的所有探针的地积
作者（S）----------Author(s)----------
Lasse Folkersen
参见----------See Also----------
geneRegionScan, plotOnGene
geneRegionScan，plotOnGene
举例----------Examples----------
data(exampleProbeLevelSet)
plotCoexpression(exampleProbeLevelSet, mrna, correlationCutoff=0.7, 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 18:59:18
