controlProbeDetection(beadarray)
controlProbeDetection()所属R语言包：beadarray
Percentage of beads detected
检测珠的百分比
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function to calculate the percentage of beads matching a defined set of control types that are detected as having intensity above background level on an array-section.
函数来计算匹配的阵列上节的强度高于背景水平的控制，检测的类型定义珠的百分比。
用法----------Usage----------
controlProbeDetection(BLData, transFun = logGreenChannelTransform, array = 1, controlProfile = NULL, tagsToDetect = list(housekeeping = "housekeeping", Biotin = "phage_lambda_genome", Hybridisation = "phage_lambda_genome:high"), negativeTag = "permuted_negative", detThresh = 0.05)
参数----------Arguments----------
参数：BLData
a beadLevelData object
beadLevelData对象
参数：transFun
transformation to be applied to data
转化为可应用于数据
参数：array
a numeric index of the array section
数字索引的数组段
参数：controlProfile
optional data frame defining ArrayAddressIDs belonging to each control type
可选的数据框属于每个控件类型定义ArrayAddressIDs
参数：tagsToDetect
vector of character strings defined which control types to interrogate
定义字符串矢量控制类型审问
参数：negativeTag
character string defining which control type to use as background
字符串定义为背景，使用的控制类型
参数：detThresh
numeric value for threshold for detection
检测阈值的数值
Details
详情----------Details----------
Details of the controls on the array-section can be inferred from the annotation of the beadLevelData object or supplied as a data frame. The first column of the data frame should contain ArrayAddressIDs, with the control type of the each ID in the second column. The strings supplied in the tagsToDetect and negativeTag parameters should be present in this column.
阵列节中的控件的细节可以推断注释beadLevelData对象或提供一个数据框。该数据框的第一列应该包含ArrayAddressIDs，在第二列中的每个ID的控制类型。所提供的字符串tagsToDetect和negativeTag参数应该是目前在此列。
The ArrayAddressIDs that correspond to the specified tags are matching to the ArrayAddressIDs for the chosen array and intensities for all beads are extracted. The function implements Illumina's method for calculating the detection scores for all bead types on a given array. Within an array, Illumina discard negative control bead-types whose summary values are more than three MADs from the median for the negative controls. Illumina then rank the summarized intensity for each other bead-type against the summarized values for the remaining negative control bead-types and calculate a detection p-value 1-R/N, where R is the relative rank of the bead intensity when compared to the $N$ remaining negative controls. Thus, if a particular bead has higher intensity than all the negative controls it will be assigned a value of 0. This calculation is repeated for all arrays.
对应到指定的标签的ArrayAddressIDs珠提取所有选择的阵列和强度ArrayAddressIDs匹配。该功能实现Illumina的所有珠类型的检测分数计算在给定的数组的方法。在一个阵列，Illumina公司丢弃阴性对照珠类型的汇总值三个以上的中位数为阴性对照MADS。 Illumina公司则排名对方珠型总结强度对其余阴性对照珠类型的汇总值计算p值1 - R / N，其中R是相对排名相比，珠强度检测$ n $其余的阴性对照。因此，如果一个特定的珠具有较高的强度比所有的阴性对照，将被分配一个0值。所有阵列重复计算。
The percentage reported is the percentage of beads of each control type that are detected at the defined threshold.
报告的百分比是每个类型定义的阈值检测控制珠子的百分比。
作者（S）----------Author(s)----------
Mark Dunning
参见----------See Also----------
beadStatusVector,calculateDetection
beadStatusVector，calculateDetection
举例----------Examples----------
if(require(beadarrayExampleData)){
data(exampleBLData)
for(i in 1:2){
print(controlProbeDetection(exampleBLData, array = i, tagsToDetect=c("housekeeping", "biotin"), negativeTag="negative"))
}
}
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 12:40:36
