backgroundEstimate(beadarraySNP)
backgroundEstimate()所属R语言包：beadarraySNP
Estimate background intensities from foreground intensity
估计从前台强度背景强度
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Background intensity from Illumina Golden Gate bead arrays are estimated based on several data models
Illumina的金门珠阵列的背景强度估计的基础上几个数据模型
用法----------Usage----------
backgroundEstimate(object,method=c("minimum", "mode","intmin",
"anglemode"), maxmode=3000, bincount=40, maxangle=0.3, subsample="OPA")
参数----------Arguments----------
参数：object
SnpSetIllumina object
SnpSetIllumina对象
参数：method
chracter, data model to use
两性间，数据模型，使用
参数：maxmode
numeric, maximum intensity for mode for method="mode"
数字模式method="mode"，最大强度
参数：bincount
numeric, for method="intmin" , see details
数字，，method="intmin"查看详细信息
参数：maxangle
numeric in radians, maximum theta for mode for method="anglemode"
数字弧度，最大THETA模式method="anglemode"
参数：subsample
factor or column name in featureData slot
featureData槽的因素或列名
Details
详情----------Details----------
The Illumina software does not provide background values in the output. Some models can be used to estimate background from the raw data intensities.<br> minimum: The allele specific minimum intensity is used.<br> mode: This model assumes that the first mode of the density of the intensities is determined by the zero-allele in the data, see ref. The signal intensity of the zero-allele should be zero, therefore this is considered the background value.<br> intmin: This model assumes there is crosstalk between the alleles, and background increases with the intensity of the other allele. The range between 0 and the maximum of the other allele is divided in bincount bins, and the minimum for this allele is determined for probes where the other allele falls in a bin. A linear fit is determined though the minimum values to obtain a gradually increasing value.<br> anglemode: This model finds the density modes closest to 0 and \frac{π}{2} for polar transformed intensities, and uses this to determine background.
Illumina公司的软件不提供输出中的背景值。一些模型可以用来估计从原始数据中强度的背景参考minimum：等位基因特异的最低发光强度是用来参考mode：该模型假设的密度模式强度由零等位基因中的数据确定，见文献。零等位基因的信号强度应该是零，因此，这被认为是背景值的参考intmin：该模型假设有之间的等位基因，并与其他等位基因力度的背景增加串扰。介于0和其他等位基因的最大范围分为bincount箱，并确定该等位基因的最低探针其他等位基因在垃圾桶内。线性拟合确定的最低值，虽然获得价值逐步增加参考anglemode：该模型认为最接近0\frac{π}{2}转化为极强度，密度模式，并使用此来确定背景。
值----------Value----------
This function returns an SnpSetIllumina object. The Rb and Gb matrices in the assayData slot contain estimated background values.
此函数返回一个SnpSetIllumina对象。 Rb和GbassayData插槽的矩阵包含估计的背景值。
作者（S）----------Author(s)----------
Jan Oosting
参见----------See Also----------
SnpSetIllumina-class, backgroundCorrect.SNP
SnpSetIllumina-class，backgroundCorrect.SNP
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。
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发表于 2012-2-25 12:34:25
