filterCtData(HTqPCR)
filterCtData()所属R语言包：HTqPCR
Filter out features (genes) from qPCR data.
从qPCR数据过滤功能（基因）。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function is for filtering Ct data from high-throughput qPCR platforms like the TaqMan Low Density Arrays. This can for example be done prior to analysing the statistical significance of the data, to remove genes where the results are of low quality, or that are not of interest to the analysis in question.
此功能是一样的TaqMan低密度阵列的高吞吐量的qPCR平台过滤CT数据。这可以例如之前完成分析数据的统计意义，以消除基因的结果是低质量的，或者是不感兴趣的问题分析。
用法----------Usage----------
filterCtData(q, remove.type, remove.name, remove.class, remove.category, n.category = 3, remove.IQR, verbose = TRUE)
参数----------Arguments----------
参数：q
object of class qPCRset.
对象类qPCRset。
参数：remove.type
character vector, the feature type(s) to be removed from the data object.
特征向量，特征类型（S）从数据对象中删除。
参数：remove.name
character vector, the feature name(s) to be removed from the data object.
特征向量，从数据对象中删除的功能名称（S）。
参数：remove.class
character vector, the feature class(es) to be removed from the data object.
特征向量，特征类（ES）被删除的数据对象。
参数：remove.category
character vector, the features categories(s) to be assessed across samples.
特征向量，（S）的功能类别横跨样品进行评估。
参数：n.category
numeric, all features with more than this number of remove.category across samples are removed.
数字，超过这个数目remove.category整个样本被删除的所有功能。
参数：remove.IQR
numeric, all features with an interquartile range (IQR) below this limit across samples will be removed.
数字，低于这个跨样本的限制与四分位距（IQR为）的所有功能将被删除。
参数：verbose
boolean, should some information be printed to the prompt.
布尔，应一些信息打印到提示。
Details
详情----------Details----------
This function may be used to exclude individual or small groups of features that are irrelevant to a given analysis. However, it can also be used on a more general basis, to for example split the data into separate qPCRset objects based on features with different characteristics, such as groups of markers or other gene classes present in featureClass.
此功能可用于排除功能，是一个给定的分析无关的个人或小团体。然而，它也可以用于更一般的基础上，例如分割成单独qPCRset对象的基础上具有不同特点的功能，如标志或其他基因类组数据呈现featureClass 。
remove.IQR can be used to exclude features that show only little variation across the samples. These are unlikely to be differentially expressed, so including them in downstream analysis such as limmaCtData or ttestCtData would result in a slight loss of power caused by the adjustment of p-values required due to multiple testing across all features.
remove.IQR可以用来排除功能，只显示整个样品几乎没有变化。这是不太可能的差异表达，其中包括在下游，如limmaCtData或ttestCtData会导致的功率略有p-值调整所造成的损失，在所有需要多个测试分析功能。
值----------Value----------
An object of class qPCRset like the input, but with the required features removed.
如输入一个类qPCRset对象，所需的功能，但删除。
注意----------Note----------
After removing features the function plotCtCard will no longer work, since the number of features is now smaller than the card dimensions.
删除功能后的功能plotCtCard将不再起作用，因为多项功能，是现在比卡尺寸小。
When using remove.category or remove.IQR and there are replicated features present on the array, it might no longer be possible to use the ndups parameter of limmaCtData, since the number of replicates isn't identical for each feature.
当使用remove.category或remove.IQR“阵列复制功能，它可能不再可能使用ndupslimmaCtData参数，自复制每个功能是不相同的。
Filtering can be performed either before or after normalization, but in some cases normalization might be affected by this, for example if many features are removed, making it difficult to identify rank-invariant genes.
过滤可以执行之前或之后的标准化，标准化，但在某些情况下可能会受此影响，许多功能，例如，如果被删除，因此很难确定排名不变的基因。
作者（S）----------Author(s)----------
Heidi Dvinge
举例----------Examples----------
# Load some example data[加载一些示例数据]
data(qPCRpros)
show(qPCRpros)
# Filter based on different feature type[筛选的基础上不同的功能类型]
qFilt <- filterCtData(qPCRpros, remove.type=c("Endogenous Control"))
# Filter based on feature type and name[筛选的基础上功能的类型和名称]
qFilt <- filterCtData(qPCRpros, remove.type=c("Endogenous Control"), remove.name=c("Gene1", "Gene20", "Gene30"))
# Filter based on feature class[基于要素类筛选]
qFilt <- filterCtData(qPCRpros, remove.class="Kinase")
# Filter based on feature categories, using two different cut-offs[过滤功能分类为基础，使用两种不同的切权衡]
qFilt <- filterCtData(qPCRpros, remove.category="Undetermined")
qFilt <- filterCtData(qPCRpros, remove.category="Undetermined", n.category=5)
# Remove features without much variation across samples[没有太多变化跨样本中删除的功能]
iqr <- apply(exprs(qPCRpros), 1, IQR, na.rm=TRUE)
hist(iqr, n=20)
qFilt <- filterCtData(qPCRpros, remove.IQR=2)
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 21:48:12
