setCategory(HTqPCR)
setCategory()所属R语言包：HTqPCR
Assign categories to Ct values from qPCR data.
qPCR数据的Ct值分配类别。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Data in qPCRset objects will have feature categories ("Unreliable", "Undetermined") assigned to them based on different Ct criteria.
qPCRset对象中的数据将有不同CT标准的基础上分配给它们的功能类别（“不可靠”，“未决定用途”）。
用法----------Usage----------
setCategory(q, Ct.max = 35, Ct.min = 10, replicates = TRUE, quantile = 0.9, groups, flag = TRUE, flag.out = "Failed", verbose = TRUE, plot = FALSE, ...)
参数----------Arguments----------
参数：q
qPCRset object.
qPCRset对象。
参数：Ct.max
numeric, the maximum tolerated Ct value. Everything above this will be "Undetermined".
数字，最大耐受Ct值。上述这一切都将是“未决定用途”。
参数：Ct.min
numeric, the minimum tolerated Ct value. Everything below this will be "Unreliable".
数字，最低容忍的Ct值。下面这一切都将是“不可靠”。
参数：replicates
logical, should Ct values from genes replicated within each sample be collapsed for the standard deviation.
逻辑，应该从每个样本内的复制基因的Ct值标准偏差倒塌。
参数：quantile
numeric from 0 to 1, the quantile interval accepted for standard deviations. See details. NULL means that variation between replicates is not used for setting the categories.
从0到1的数字，位数区间标准偏差为接受。查看详情。 NULL意味着没有设置类别之间的复制变异。
参数：groups
vector, grouping of cards, for example biological or technical replicates. NULL means that variation between groups os samples is not assessed, same as for setting quantile=NULL.
向量，卡分组，例如生物或技术复制。 NULL意味着该组OS样本之间的变化不评估，设置quantile=NULL相同。
参数：flag
logical, should categories also be set to "Unreliable" according to the content of flag(q).
逻辑，类别也可以设置为“不可靠”根据内容flag(q)。
参数：flag.out
character vector, if flag=TRUE, what are the flag(s) to be set as "Unreliable".
特征向量，如果flag=TRUE，什么是必须设置为“不可靠”的标志（S）。
参数：verbose
logical, should a summary about category counts per sample be printed to the prompt.
逻辑，应该被打印到大约每个样本的类别计数摘要提示。
参数：plot
logical, should some plots of the standard deviations be created.
逻辑，应该创建标准差一些图。
参数：...
any other arguments are passed to plot.
任何其他的参数被传递到plot。
Details
详情----------Details----------
Categories can be assigned to the featureCategory of the qPCRset using either just simple criteria (max/min of Ct values or flag of q) or by looking at the standard deviation of Ct values across biological and technical replicates for each gene.
featureCategory的qPCRset要么只是简单的标准（CT值的最大/最小或flagq）或看着对面的Ct值的标准偏差可以被分配到分类生物技术为每一个基因的复制。
When looking at replicates, the standard deviation and mean are calculated and a normal distribution following these parameters is generated. Individual Ct values that are outside the interval set by quantile are set as "Unreliable". So if e.g. quantile=90 the values outside the top 5% and lower 5% of the normal distribution with the given mean and standard deviation are removed.
在复制时，标准偏差和平均计算，生成后，这些参数正态分布。个别的Ct值是外quantile间隔设置为“不可靠”。因此，如果如quantile=90值以外的前5％和低5％，与给定的均值和标准差的正态分布被删除。
"Undetermined" has priority over "Unreliable", so if a value is outside quantile but also above Ct.max it will be "Undetermined".
“未决定用途”超过“不可靠”的优先级，因此，如果一个值外quantile但也高于Ct.max“这将是”未决定用途“。
NB: When setting categories based on replicates, the Ct values are assumed to follow a normal distribution. This might not be the case if the number of samples within each group is small, and there are no replicates on the genes within each sample.
注：当设置上复制的类别，Ct值被假定服从正态分布。如果每个组内的样本数量很小的情况下，这可能不是，有没有在每个样品中的基因复制。
If the number of replicates vary significantly between biological groups, this will influence the thresholds used for determining the range of "OK" Ct values.
如果复制的数量，生物群体之间的显着变化，这将影响决定“确定”Ct值范围内使用的阈值。
值----------Value----------
If plot=TRUE one figure per sample grous is returned to the current graphics device.
如果plot=TRUE每一个样品grous数字则返回到当前图形设备。
注意----------Note----------
It's adviced to try several different values for quantile, depending on the input data set. Using the function PlotCtCategory(..., by.feature=FALSE) or plotCtCategory(..., by.feature=TRUE) might help assess the result of different quantile choices.
它谏quantile根据输入的数据集，尝试几个不同的值。使用功能PlotCtCategory(..., by.feature=FALSE)或plotCtCategory(..., by.feature=TRUE)可能有助于评估不同quantile选择的结果。
作者（S）----------Author(s)----------
Heidi Dvinge
参见----------See Also----------
filterCategory, plotCtCategory
filterCategory，plotCtCategory
举例----------Examples----------
# Load example data[加载示例数据]
data(qPCRraw)
exFiles <- read.delim(file.path(system.file("exData", package="HTqPCR"), "files.txt"))
# Set categories in various ways[设置在各种方式的类别]
setCategory(qPCRraw, flag=FALSE, quantile=NULL)
setCategory(qPCRraw[,1:4], groups=exFiles$Treatment[1:4], plot=TRUE)
setCategory(qPCRraw[,1:4], groups=exFiles$Treatment[1:4], plot=TRUE, quantile=0.80)
x <- setCategory(qPCRraw, groups=exFiles$Treatment, verbose=FALSE, quantile=0.80)
# Plot the categories[绘制的类别]
plotCtCategory(x)
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 21:52:40
