peaklist-class(IPPD)
peaklist-class()所属R语言包：IPPD
"Peaklist"
“Peaklist”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Object returned from a call to getPeaklist.
对象返回从调用getPeaklist到。
插槽----------Slots----------
peaklist A matrix with rows equal to the number of peak patterns used in fitting and five columns. For each row (pattern), the first column contains the initial position of the peak pattern (loc_init, in Thomson), the second one contains the position of the most intense peak within a peak pattern (loc_most_intense, in Thomson), the third one contains the charge state (charge), the fourth one the quantification of the overall intensity of the pattern (quant) and the last
一个用于装修和五列的高峰模式的数量相等的行peaklist matrix。对于每一行（模式），第一列包含的峰值模式的初始位置（loc_init，汤姆逊），第二个是包含在峰值模式的最激烈的峰值位置（loc_most_intense ，汤姆逊），第三个包含充电状态（charge），第四个量化的整体格局强度（quant）和最后
peaklistprocessed The result after applying the postprocessing procedure to the raw list peaklist. It is a matrix of the same structure as peaklist, with two up to four additional columns: the fifth column contains the local noise level at the position, and the last one contains the ratio of the amplitude to local noise level (signal-to-noise ratio), hence quantitatively describing the significance of the peak pattern. If goodnessoffit has been set to TRUE, there are two additional columns labelled goodness_of_fit and ratio_adj. The column goodness_of_fit contains a local assessment of the goodness-of-fit at the respective positions in the spectrum, while the column ratio_adj contains a goodness-of-fit adjusted signal-to-noise ratio. If postprocessed has been set to FALSE
peaklistprocessed的申请后处理程序的原始列表peaklist后的结果。这是一个矩阵相同的结构peaklist，有两个附加列四个：第五列中包含的地方的噪音水平，在这个位置上，最后一个包含幅度比当地的噪音水平（信号噪声比），因此，定量描述的峰值模式的意义。 goodnessoffit如果已被设置为TRUE，有两个额外的列标记goodness_of_fit和ratio_adj。列goodness_of_fit包含了当地的评估善良适合在频谱各自的立场，而列ratio_adj包含一个善良的拟合调整的信号噪声比。如果postprocessed已FALSE
model One of "Gaussian" or "EMG".
“高斯”或“肌电图”的模型之一。
loss One of "L2" or "L1".
“二级”或“母语”的损失之一。
alpha Function for the parameter "alpha" (model = "EMG").
阿尔法功能参数的“阿尔法”（model = "EMG"）。
sigma Function for the parameter "sigma" (both models).
西格玛“西格玛”（两种型号）为参数的函数。
mu Function for the parameter "mu" (model = "EMG").
亩函数参数“亩”（model = "EMG"）。
charges A numeric vector containing the set of charge states used.
收取一个numeric向量组的负责国家使用。
basis The matrix of basis functions if returnbasis has been set to TRUE when calling getPeaklist. Otherwise,
基础矩阵的基础功能，如果returnbasis已设置为TRUE当调用getPeaklist。否则，
book A matrix annotating each column of basis. Each row corresponds to a template/peak pattern characterized by the initial position of the peak pattern (column initial), the position of the most intense peak (column most_intense) and the charge
书matrixbasis注释每个列。每一行对应于模板/峰峰值模式的初始位置（列initial），最激烈的高峰位置（列most_intense）和负责的模式
beta A numeric vector storing the amplitudes for each peak pattern in book/each column of basis, obtained by non-negative least squares estimation (if loss = "L2") or by non-negative least absolute deviation estimation (if loss = "L1"). Hence, together with book,
测试一个numeric向量存储振幅为每个峰的格局book/每列basis，获得非负最小二乘估计（如果loss = "L2"），或由非负最小绝对偏差估计（如果loss = "L1"）。因此，连同book，
locnoise A matrix of local quantiles of the intensities computed along the spectrum. Each row corresponds to a m/z value of the spectrum (ordered increasingly), and each column to a quantile as indicated by the column names. For instance, slot(object,
沿频谱的强度计算的本地位数locnoise一个matrix。每一行对应的是/ z值的频谱（越来越下令），每个分量的列列名表示。例如中，<code>插槽（对象，
noiselevel A numeric vector storing the noise level used for computation of the
noiselevel一个numeric向量用于存储的噪音水平计算
goodnessoffit A numeric vector storing the local goodness-of-fit criterion. An empty vector unless control.postprocessing$goodnessfittrue was
goodnessoffit一个numeric向量存储在本地的善良的适合的标准。除非control.postprocessing$goodnessfittrue是一个空向量
data A list storing the spectrum used to generate the object.
数据list存储用于生成对象的频谱。
方法----------Methods----------
show Use show(object) for brief information about the
显示使用有关的简短信息show(object)
threshold Only applicable if postprocessed has been set to TRUE when calling getPeaklist. A function to threshold peaklistprocessed, yielding a peaklist maintaining only those peaks exceeding a specified threshold. Optionally, re-fitting of the spectrum using only those templates that have passed the thresholding step can be performed. The argument list is given by
阈值仅适用于postprocessed如果已被设置为TRUE当调用getPeaklist。一个阈值函数peaklistprocessed，产生peaklist的维护只有那些超过指定的阈值的峰值。或者，重新装修的频谱使用，只有那些通过阈值的步骤模板可以执行。参数列表
object An object of class peaklist.
object类peaklist的对象。
threshold The value to be used as threshold.
threshold值作为阈值。
ratio Whether to use the signal-to-noise ratio "ratio" or the goodness-of-fit adjusted signal-to-noise ratio
ratio是否使用信号信噪比"ratio"或善良适合调整的信号噪声比
refit Whether re-fitting of the spectrum should be done,
refit重新装修的频谱是否应做的，
trace A logical indicating whether information tracing the different steps of the
traceAlogical指示是否跟踪的不同步骤的信息
eps Function values below eps are set equal to
eps下面eps函数值设置等于
.
。
visualize A function to displaying the results of the fitting procedure, in particular significant peak patterns, in selected m/z ranges. The description of the arguments is as follows:
可视化展示装修过程的结果，特别是显着的峰值模式，在选定的的m / z范围的功能。参数说明如下：
object An object of class peaklist.
object类peaklist的对象。
mz The vector of m/z values used to obtain object.
mz用于获取objectm / z值的向量。
intensities The vector of intensities used to obtain object.
intensities用于获取object强度向量。
lower, upper The m/z range for which the result of the fitting procedure should be visualized (lower < upper). Hint: the difference upper - lower should be between 0-30. If it is significantly larger, computation times increase considerably. Moreover, this will lead to a reduced
lower, upperm / z范围为装修过程的结果应该是可视化（lower < upper）。提示：区别upper - lower应在0-30之间。如果是明显较大，计算时间大大增加。此外，这将导致减少
truth May be set to TRUE if one has a precise knowledge of the true underlying signal (normally only occuring for simulated data) and one wants to compare the results with the gold standard. If truth = TRUE, booktrue (s. below) has to be specified. In this case, the true signal is displayed as upper panel
truth可设置为TRUE如果一个人有一个真正的底层信号的精确知识（通常只用于模拟数据发生），并希望与金标准比较的结果。如果truth = TRUE，booktrue（S.下面）必须指定。在这种情况下，真正的信号显示为上游面板
signal A logical indicating whether the raw spectrum in the range [lower,upper] should be plotted. If TRUE, it is displayed as upper panel or as one
signalAlogical原始频谱范围内的[lower,upper]是否应绘制。如果TRUE，它显示面板上或作为一个
fitted A logical indicating whether basically all (with restrictions, s. cutoff.functions and cutoff.eps below) fitted templates should be plotted. If TRUE, the result is displayed as a middle
fittedAlogical指示是否基本上所有的限制。cutoff.functions和cutoff.eps下面装模板应绘制。如果TRUE，结果显示作为一个中等
postprocessed A logical indicating whether fitted templates after postprocessing should be
postprocessedAlogical指示装后的后处理模板是否应该
fittedfunction A logical indicating whether the fitted function should be drawn as lines in the panel displaying the raw spectrum (requires signal = TRUE). Note that the fitted function is the result of summing up all fitted templates multiplied by their amplitude. Setting fittedfunction = TRUE requires that object contains the
fittedfunctionAlogical指示是否应在原始频谱显示面板线绘制拟合函数（signal = TRUE）。请注意，拟合函数是总结乘以其幅度都装模板的结果。设置fittedfunction = TRUE要求object包含
fittedfunction.cut A logical indicating whether the fitted function after cutting peak patterns falling below a prespecified cutoff should be drawn as lines in the panel displaying the raw spectrum (requires signal = TRUE). Setting fittedfunction.cut = TRUE requires that object contains the
fittedfunction.cutAlogical指示后，削减峰值下降低于预先设定的截止模式的拟合函数是否应作为原始频谱显示面板中的行画（signal = TRUE）。设置fittedfunction.cut = TRUE要求object包含
quantile Optional argument. If quantile is specified, it has to be one of the values 0.1,...,0.9, and the corresponding local quantile as contained in the slot locnoise
quantile可选参数。如果quantile指定的，它必须是一个值0.1,...,0.9，以及相应的地方位数插槽locnoise所载
booktrue Required if and only if truth = TRUE. In this case, booktrue has to be a matrix having the same structure as cbind(slot(object, "book"), slot(object, "beta")), i.e. the first two columns of booktrue contain initial- and most intense peak locations within a peak pattern, the third column contains the charge state and the fourth one the amplitude of the most intense peak. Note: the 'truth' is computed according to slot(object, model). This excludes the following scenario: assuming that the true peak shapes is "EMG", but the chosen model is "Gaussian". Then the true model in this function is
booktrue当且仅当truth = TRUE需要。在这种情况下，booktrue是一个矩阵，具有相同的结构cbind(slot(object, "book"), slot(object, "beta"))，即前两列booktrue包含初始和最激烈的峰值位置，在繁忙的模式第三列包含的电荷态和第四个最激烈的峰值幅度。注：真理计算根据slot(object, model)。这不包括以下情形：假设，真正的峰形"EMG"，但所选择的模式是"Gaussian"。然后在这个函数中的真实模型
cutoff.eps, cutoff.functions Control arguments reducing the number of templates to be plotted if fitted = TRUE. Specifying cutoff.eps removes all templates with intensity smaller than cutoff.eps. Specifying cutoff.functions as a positive
如果cutoff.eps, cutoff.functionsfitted = TRUE控制参数，减少模板的数量要绘制。指定cutoff.eps强度比cutoff.eps小删除所有模板。指定cutoff.functions作为一个积极
... Additional options passed to plot.
...附加选项传递给plot。
Note that the colours in the plot have no meaning. They are only used to distinguish between different patterns within a panel. Further note that the colour of a pattern appearing in several panels may vary from panel to panel.
请注意，在图的颜色没有任何意义。他们只是用来区分不同的模式在一个小组。进一步说明，一个模式出现在几个面板的颜色可能会有所不同，从面板到面板。
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。
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发表于 2012-2-25 22:25:27
