TRAMP(TRAMPR)
TRAMP()所属R语言包：TRAMPR
TRFLP Analysis and Matching Program
TRFLP分析与匹配程序
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Determine if TRFLP profiles may match those in a database of knowns. The resulting object can be used to produce a presence/absence matrix of known profiles in environmental samples.
确定，如果TRFLP配置文件可能与那些在数据库中的已知。将得到的对象可以被用来产生已知公司环境样品中的存在/不存在矩阵。
The TRAMPR package contains a vignette, which includes a worked example; type vignette("TRAMPRdemo") to view it.
TRAMPR包中包含一个小插曲，其中包括一个工作的例子;类型vignette("TRAMPRdemo")查看它。
用法----------Usage----------
TRAMP(samples, knowns, accept.error=1.5, min.comb=4, method="maximum")
参数----------Arguments----------
参数：samples
A TRAMPsamples object, containing unidentified samples.
ATRAMPsamples对象，含有不明身份的样本。
参数：knowns
A TRAMPknowns object, containing identified TRFLP patterns.
ATRAMPknowns对象，包含确定TRFLP模式。
参数：accept.error
The largest acceptable difference (in base pairs) between any peak in the sample data and the knowns database (see Details; interpretation will depend on the value of method).
可接受的最大区别（碱基对）之间的样本数据和已知的高峰数据库（见详情;解释将取决于值的method）。
参数：min.comb
Minimum number of enzyme/primer combinations required before presence will be tested. The default (4) should be reasonable in most cases. Setting min.comb to NA will require that all enzyme/primer combinations in the knowns database are present in the samples.
酶/引物组合之前存在的最小数量将受到考验。在大多数情况下，应该是合理的默认值（4）。设置min.combNA将要求所有的酶/引物组合在已知数据库的样本中。
参数：method
Method used in calculating the difference between samples and knowns; may be one of "maximum", "euclidian" or "manhattan" (or any unambiguous abbreviation).
使用的方法计算样品和已知的区别，可能是"maximum"，"euclidian"或"manhattan"（或任何明确的缩写）。
Details
详细信息----------Details----------
TRAMP attempts to determine which species in the "knowns" database may be present in a collection of samples.
TRAMP尝试，以确定哪些物种在“已知的数据库中，可以是本中的样本的集合。
A sample matches a known if it has a peak that is “close enough” to every peak in the known for every enzyme/primer combination that they share. The default is to accept matches where the largest distance between a peak in the knowns database and the sample is less than accept.error base pairs (default 2), and where at least min.comb enzyme/primer combinations are shared between a sample and a known (default 4).
的样本相匹配的，如果它有一个峰值，是“足够接近”的每一个酶/引物组合，他们的每一个高峰期。默认值是接受匹配已知数据库中的峰值和样品间的最大距离是小于accept.error的碱基对（默认为2），并在至少min.comb酶/引物组合共享之间的样本和公知的（默认为4）。
The three-dimensional matrix of match errors is generated by create.diffsmatrix. In the resulting array, m[i,j,k] is the difference (in base pairs) between the ith sample and the jth known for the kth enzyme/primer combination.
三维矩阵的匹配误差的是，所产生的create.diffsmatrix。以所得的数组，m[i,j,k]是i个采样和j第k个酶/引物组合的已知的差异（以碱基对为单位）之间。
If p_k and q_k are the sizes of peaks for the kth enzyme/primer combination for a sample and known (respectively), then maximum distance is defined as
如果p_k和q_kk个酶/引物组合的样品和已知的（分别）的峰值的大小，然后最大距离被定义为
Euclidian distance is defined as
欧几里得距离被定义为
and Manhattan distance is defined as
和曼哈顿距离被定义为
where n is the number of shared enzyme/primer combinations, since this may vary across sample/known combinations. For Euclidian and Manhattan distances, accept.error then becomes the mean distance, rather than the total distance.
n是共享的酶/引物组合，因为这可能会有所不同样品/已知的组合。欧几里德和曼哈顿距离，accept.error然后成为的平均距离，而不是总距离。
值----------Value----------
A TRAMP object, with elements:
ATRAMP对象的元素：
参数：presence
Presence/absence matrix. Rows are different samples (with rownames from labels(samples)) and columns are different knowns (with colnames from labels(knowns)). Do not access the presence/absence matrix directly, but use summary.TRAMP, which provides options for labelling knowns, grouping knowns, and excluding “ignored” matches.
存在/不存在的矩阵。行是不同的样品（行名来自不同的已知labels(samples)）和列（列名labels(knowns)）。不要直接访问存在/不存在矩阵，但使用summary.TRAMP，它提供标签已知的选项，分组已知，和排除“忽略”比赛。
参数：error
Matrix of distances between the samples and known, calculated by one of the methods described above. Rows correspond to different samples, and columns correspond to different knowns. The matrix dimension names are set to the values sample.pk and knowns.pk for the samples and knowns, respectively.
样本之间的和已知的，由上述的方法之一，计算出的距离矩阵。行对应于不同的样品，和列相对应的不同的已知。矩阵维数名sample.pk和knowns.pk用于样品和已知，分别设置为值。
参数：n
A two-dimensional matrix (same dimensions as error), recording the number of enzyme/primer combinations present for each combination of samples and knowns.
一个二维矩阵（如error），记录的酶/引物组合的数目存在样品和已知的每一种组合的尺寸相同。
参数：diffsmatrix
Three-dimensional array of output from create.diffsmatrix.
三维阵列输出从create.diffsmatrix。
参数：enzyme.primer
Different enzyme/primer combinations present in the data, in the order of the third dimension of diffsmatrix (see create.diffsmatrix for details).
不同的酶/引物组合中存在的数据，在diffsmatrix（见create.diffsmatrix）的第三个维度的顺序。
参数：samples, knowns, accept.error, min.comb, method
The input data objects and arguments, unmodified.
输入的数据对象和参数，不作修改。
In addition, an element presence.ign is included to allow matches to be ignored. However, this interface is experimental and its current format should not be relied on - use remove.TRAMP.match rather than interacting directly with presence.ign.
此外，一个元素presence.ign是包含允许匹配被忽略。但是，这个接口是实验性的，不应该依赖于目前的格式 - 使用remove.TRAMP.match，而不是直接交互与presence.ign的。
Matching is based only on peak size (in base pairs), and does not consider peak heights.
匹配的基础上峰的大小（碱基对），不考虑峰值的高度。
参见----------See Also----------
See create.diffsmatrix for discussion of how differences between sample and known profiles are generated.
见create.diffsmatrix讨论的样品和已知的配置文件之间的差异是如何产生的。
plot.TRAMP, which displays TRAMP fits graphically.
plot.TRAMP，适合图形化显示TRAMP。
summary.TRAMP, which creates a presence/absence matrix.
的summary.TRAMP，它创建了一个存在/不存在矩阵。
remove.TRAMP.match, which marks TRAMP matches as ignored.
remove.TRAMP.match，这标志着TRAMP的匹配，而忽略。
实例----------Examples----------
data(demo.knowns)
data(demo.samples)
res <- TRAMP(demo.samples, demo.knowns)
## The resulting object can be interrogated with methods:[＃生成的对象可以询问使用方法：]
## The goodness of fit of the sample with sample.pk=101 (see[＃善良的适合的样本与sample.pk = 101的（见]
## ?\link{plot.TRAMP}).[＃\链接{plot.TRAMP}）。]
plot(res, 101)
## Not run: [＃不运行：]
## To see all plots (this produces many figures), one after another.[＃查看所有图（这将产生许多数字），一个又一个的。]
op <- par(ask=TRUE)
plot(res)
par(op)
## End(Not run)[＃（不执行）]
## Produce a presence/absence matrix (see ?\link{summary.TRAMP}).[＃存在/不存在的矩阵（看到了吗？\的链接{summary.TRAMP}）。]
m <- summary(res)
head(m)
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 2012-10-1 11:44:17
