getDynamicRange(cellHTS2)
getDynamicRange()所属R语言包：cellHTS2
Per-plate dynamic range of a cellHTS object
每板的动态范围一个cellHTS对象
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Calculates per-plate dynamic range of data stored in a cellHTS object.
计算每盘动态cellHTS对象中存储的数据的范围。
用法----------Usage----------
getDynamicRange(x,
verbose=interactive(),
definition,
posControls,
negControls)
参数----------Arguments----------
参数：x
a configured cellHTS object. See details.
配置的cellHTS对象。查看详情。
参数：verbose
a logical, if TRUE the function reports some of its intermediate progress. The default is the state of interactive().
一个逻辑，如果TRUE功能报告及其中间体的一些进展。默认是状态interactive()。
参数：definition
a character string with possible values "ratio" or "difference". See details.
一个可能值“比”或“差”的字符串。查看详情。
参数：posControls
(optional) a list or vector of regular expressions specifying the name of the positive controls. See details.
（可选）列表或指定名称的阳性对照的正则表达式的向量。查看详情。
参数：negControls
(optional) a vector of regular expressions specifying the name of the negative controls. See details.
（可选）一个向量的正则表达式指定名称的阴性对照。查看详情。
Details
详情----------Details----------
x should be an already configured cellHTS object (state(x)["configured"]=TRUE), so that the information about the well annotation of the plates is available.
x应该是一个已配置cellHTS对象（state(x)["configured"]=TRUE），使板块以及注解有关的信息可用。
The per-plate dynamic ranges are calculated for the data stored in slot assayData of x. This can be raw data, normalized data or scored data.
每板的动态范围计算的数据存储在插槽assayDatax的。这可能是原始数据，规范化的数据或取得的数据。
If definition="difference", the dynamic range is calculated as the absolute difference between the arithmetic average on positive and negative controls.
如果definition="difference"，作为阳性和阴性对照的绝对差值之间的算术平均计算的动态范围。
If definition="ratio", the dynamic range is calculated as the ratio between the geometric mean on positive and negative controls.
如果definition="ratio"，作为阳性和阴性对照的几何平均数之间的比例计算的动态范围。
NOTE: the argument definition should only be set to "ratio" if data are in positive scale!
注：如果数据是积极的规模，参数definition只应设置为"ratio"！
If definition is missing it is determined based on the scale of the data. By default, if data are in positive scale, definition is set to "ratio", otherwise, it is set to "difference".
如果definition缺少数据规模的基础上确定。默认情况下，如果阳性规模数据，定义设置"ratio"，否则，它被设置为"difference"。
posControls and negControls should be given as a vector of regular expression patterns specifying the name of the positive(s) and negative(s) controls, respectivey, as provided in the plate configuration file (and accessed via wellAnno(x)). The length of these vectors should be equal to the current number of channels in x (dim(Data(x))[3]). By default, if posControls is not given, pos will be taken as the name for the wells containing positive controls. Similarly, if negControls is missing, by default neg will be considered as the name used to annotated the negative controls. The content of posControls and negControls will be passed to regexpr for pattern matching within the well annotation given in wellAnno(x) (see examples). If no controls are available for a given channel, use "" or NA for that channel. For example, posControls = c("", "(?i)^diap$") means that channel 1 has no positive controls, while diap is the positive control for channel 2.
posControls和negControls应作为向量的正则表达式模式（S）的积极和消极的（S）控制，respectivey板配置文件的规定，（和访问指定的名称通过wellAnno(x)）。这些向量的长度应该等于渠道目前在x（dim(Data(x))[3]）。默认情况下，如果posControls没有给出，pos将被视为包含阳性对照井的名字。同样，如果negControls缺少，默认的neg将被视为注明阴性对照用的名称。 posControls和negControls将传递给regexpr在wellAnno(x)（见例子）给出了很好的注释模式匹配的内容。如果没有控制对于一个给定的通道，该通道使用""或NA。例如，posControls = c("", "(?i)^diap$")1通道意味着没有阳性对照，而diap是通道2的阳性对照。
The arguments posControls and negControls are particularly useful in multi-channel data since the controls might be reporter-specific, or after normalizing multi-channel data.
论据posControls和negControls是特别有用的，因为在多通道数据的控制可能是特定的记者，或标准化后多通道数据。
If there are different positive controls, the dynamic range is calculated between each of the positive controls and the negative controls.
如果有不同的阳性对照，计算每个阳性对照和阴性对照之间的动态范围。
In the case of a two-way assay, where two types of "positive" controls are used in the screen ("activators" and "inhibitors"), posControls should be defined as a list with two components (called act and inh), each of which should be vectors of regular expressions of the same length as the current number of reporters (as explained above). The dynamic range is calculated between each type of positive control (activators or inhibitors) and the negative controls.
在双向检测，在屏幕上使用两种类型的“积极”的控制（“激活”和“抑制剂”），posControls应作为一个列表定义有两个组件的情况下（称为act和inh），其中每一个应该作为当前的记者人数（如上所述）的相同长度的正则表达式的向量。动态范围计算彼此之间阳性对照（activators或inhibitors）和阴性对照。
值----------Value----------
The function generates a list with the per-plate dynamic ranges in each channel and each replicate. The average dynamic range between replicates is also given. Each element of this list is an array of dimensions nrPlates x (nrReplicates + 1) x nrChannels, and is named by the positive controls. In the case of a two-way assay, these elements are called activators and inhibitors, while for a one-way assay, the elements have the same name of the positive
函数生成一个与每个通道中的每板的动态范围和每个重复的名单。也给出了平均动态范围之间复制。此列表中的每个元素是一个数组的维nrPlates x (nrReplicates + 1) x nrChannels，被命名阳性对照。在双向检测的情况下，这些元素被称为activators和inhibitors，而对于一个单向检测，元素的名称相同的积极
作者（S）----------Author(s)----------
Ligia P. Bras <a href="mailto:ligia@ebi.ac.uk">ligia@ebi.ac.uk</a>
参考文献----------References----------
screens, Genome Biology 7, R66.
参见----------See Also----------
configure, writeReport
configure，writeReport
举例----------Examples----------
data(KcViabSmall)
## pCtrls <- c("pos") [＃pCtrls < - C（“POS”）]
## nCtrls <- c("neg") [＃nCtrls < - C（“负”）]
## or for safety reasons (not a problem for the current well annotation, however) [＃或出于安全的原因（不是问题，但是当前以及注解）]
pCtrls <- c("^pos$")
nCtrls <- c("^neg$")
dr <- getDynamicRange(KcViabSmall, definition="ratio", posControls=pCtrls, negControls=nCtrls)
## same as: [＃一样的：]
## getDynamicRange(KcViabSmall)[＃getDynamicRange（KcViabSmall）]
x <- normalizePlates(KcViabSmall, scale="multiplicative", log=TRUE, method="median", varianceAdjust="none")
try(drn <- getDynamicRange(x, definition="ratio"))
drn <- getDynamicRange(x, definition="difference")
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 14:15:45
