TRAMPknowns(TRAMPR)
TRAMPknowns()所属R语言包：TRAMPR
TRAMPknowns Objects
TRAMPknowns对象
译者：生物统计家园网 机器人LoveR
描述----------Description----------
These functions create and interact with TRAMPknowns objects (collections of known TRFLP patterns). Knowns contrast with “samples” (see TRAMPsamples) in that knowns contain identified profiles, while samples contain unidentified profiles. Knows must have at most one peak per enzyme/primer combination (see Details).
这些功能和互动TRAMPknowns对象（集合已知的TRFLP模式）。已知的对比与“样本”（见TRAMPsamples）中，已知包含确定的配置文件，而样品中含有不明身份的配置文件。知道必须至多有一个峰值，根据酶/引物组合（见详情）。
用法----------Usage----------
TRAMPknowns(data, info, cluster.pars=list(), file.pat=NULL,
warn.factors=TRUE, ...)
## S3 method for class 'TRAMPknowns'
labels(object, ...)
## S3 method for class 'TRAMPknowns'
summary(object, include.info=FALSE, ...)
参数----------Arguments----------
参数：data
data.frame containing peak information.
数据框包含峰值信息。
参数：info
data.frame, describing individual samples (see Details for definitions of both data.frames).
数据框，说明个别样品（见详情的定义都data.frames的）。
参数：cluster.pars
Parameters used when clustering the knowns database. See Details.
时使用的参数聚类已知数据库。查看详细信息。
参数：file.pat
Optional partial filename in which to store knowns database after modification. Files <file.pat>_info.csv and <file.pat>_data.csv will be created.
可选部分在其中存储已知的数据库修改后的文件名。文件<file.pat>_info.csv和<file.pat>_data.csv将被创建。
参数：warn.factors
Logical: Should a warning be given if any columns in info or data are converted into factors?
逻辑：应给予警告，如果任何列在info或data被转换成因素？
参数：object
A TRAMPknowns object.
ATRAMPknowns对象。
参数：include.info
Logical: Should the output be augmented with the contents of the info component of the TRAMPknowns object?
逻辑：输出增强与info组成部分TRAMPknowns对象的内容吗？
参数：...
TRAMPknowns: Additional objects to incorportate into a TRAMPknowns object. Other methods: Further arguments passed to or from other methods.
TRAMPknowns：额外的的对象的incorportate成TRAMPknowns对象。其他方法：通过进一步的论据或其他方法。
Details
详细信息----------Details----------
The object has at least two components, which relate to each other (in the sense of a relational database). info holds information about the individual samples, and data holds information about individual peaks (many of which may belong to a single sample).
该对象至少有两个组件，这些组件之间的相互关系（在这个意义上的关系型数据库）。 info持有的个别样本的信息，和data持有个人信息峰（其中许多属于单个样品）。
Column definitions:
列定义：
info:
info：
knowns.pk: Unique positive integer, used to identify
knowns.pk：唯一的正整数，用于标识
species: Character, giving species name.
species：性格，给物种的名称。
data:
data：
knowns.fk: Positive integer, indicating which sample the peak belongs to (by matching against info$knowns.pk)
knowns.fk：正整数，表示样品的峰属于（匹配对info$knowns.pk）
primer: Character, giving the name of the primer
primer：字符，给出的引物的名称
enzyme: Character, giving the name of the
enzyme：字符，提供的名称
size: Numeric, giving size (in base pairs) of the
size：数字，使大小（碱基对）的
In addition, TRAMPknowns will create additional columns holding clustering information (see group.knowns). Additional columns are allowed (and retained, but ignored) in both data.frames. Additional objects are allowed as part of the TRAMPknowns object, but these will not be written by write.TRAMPknowns; any extra objects passed (via ...) will be included in the final TRAMPknowns object.
此外，TRAMPknowns将创建额外的列，持有聚类信息（见group.knowns）。允许其他列（保留，但忽略不计）在这两个data.frames。其他对象的TRAMPknowns对象的一部分，是允许的，但不会写的write.TRAMPknowns，通过任何额外的对象（通过...）将被包含在最终TRAMPknowns 对象。
The cluster.pars argument controls how knowns will be clustered (this will happen automatically as needed). Elements of the list cluster.pars may be any of the three arguments to group.knowns, and will be used as defaults in subsequent calls to group.knowns. If not provided, default values are: dist.method="maximum", hclust.method="complete", cut.height=2.5 (if only some elements of cluster.pars are provided, the remaining elements default to the values above). To change values of clustering parameters in an existing TRAMPknowns object, use group.knowns.
cluster.pars参数控制，如何已知将聚类（这将自动发生，需要的话）。列表中cluster.pars的元素可以是任何的三个参数group.knowns，并会被用来作为默认值的后续调用group.knowns。如果没有提供，默认值是：dist.method="maximum"，hclust.method="complete"，cut.height=2.5（如果只有某些元素cluster.pars提供，其余的元素默认的值）。要更改聚类参数的值在现有的TRAMPknowns对象中，使用group.knowns。
A known contains at most one peak per enzyme/primer combination. Where a species is known to have multiple TRFLP profiles, these should be treated as separate knowns with different, unique, knowns.pk values, but with identical species values. A sample containing either pattern will then be recorded as having that species present (see group.knowns).
一个已知的最多包含一个峰值，根据酶/引物组合。当一个物种被称为，有多个TRFLP配置文件，这些应被视为独立的已知不同的，独特的，knowns.pk值，但具有相同的species值。一试样含有两个指令模式将被记录有该物种目前（见group.knowns“）。
值----------Value----------
参数：TRAMPknowns
A new TRAMPknowns object: a list with components info, data (the provided data.frames, with clustering information added to info), cluster.pars and file.pat, plus any extra objects passed as ....
一个新的TRAMPknowns对象：组件的列表info，data（提供data.frames，聚类信息添加到info）cluster.pars和 file.pat，以及任何额外的对象...。
参数：labels.TRAMPknowns
A sorted vector of the unique samples present in x (from info$knowns.pk).
的排序向量的独特样本出现在x（info$knowns.pk）。
参数：summary.TRAMPknowns
A data.frame, with the size of the peak (if present) for each enzyme/primer combination, with each known (indicated by knowns.pk) as rows and each combination (in the format <primer>_<enzyme>) as columns.
甲数据框，与为每个酶/引物组合（如果存在的话）的峰值的大小，与每个已知（表示由knowns.pk）作为行和每个组合（在格式<primer>_<enzyme>）作为列。
注意----------Note----------
Across a TRAMPknowns object, primer and enzyme names must be exactly the same (including case and whitespace) to be considered the same. For example "ITS4", "Its4", "ITS 4" and "ITS4 " would be considered to be four different primers.
在整个TRAMPknowns对象，引物和酶的名称必须完全相同（包括案例和空白的）被认为是相同的。例如"ITS4"，"Its4"，"ITS 4"和"ITS4 "将被认为是四个不同的引物。
Factors will not merge correctly (with combine.TRAMPknowns or add.known). TRAMPknowns will attempt to catch factor columns and convert them into characters for the info and data data.frames. Other objects (passed as part of ...) will not be altered.
因素将无法正确合并（combine.TRAMPknowns或add.known）。 TRAMPknowns将尝试，赶上因素列，并将其转换成字符info和datadata.frames。其他对象（通过为部分...）不会被改变。
参见----------See Also----------
TRAMPsamples, which constructs an analagous object to hold “samples” data.
TRAMPsamples，构造一个analagous的对象来保存“样本”数据。
plot.TRAMPknowns, which creates a graphical representation of the knowns data.
的plot.TRAMPknowns，它创建了一个图形表示的已知数据。
TRAMP, for matching unknown TRFLP patterns to TRAMPknowns objects.
TRAMP，为匹配未知TRFLP的模式，以TRAMPknowns对象。
group.knowns, which groups similar knowns (generally called automatically).
group.knowns，将相似的已知（通常被称为自动）。
add.known and combine.TRAMPknowns, which provide tools for adding knowns from a sample data set and merging knowns databases.
add.known和combine.TRAMPknowns，它提供的工具从样本数据集，并添加已知，已知的数据库合并。
实例----------Examples----------
## This example builds a TRAMPknowns object from completely artificial[＃这个例子建立一个TRAMPknowns，对象完全是人为的]
## data:[＃数据：]
## The info data.frame:[＃信息数据框：]
knowns.info <-
data.frame(knowns.pk=1:8,
species=rep(paste("Species", letters[1:5]), length=8))
knowns.info
## The data data.frame:[＃数据数据框：]
knowns.data <- expand.grid(knowns.fk=1:8,
primer=c("ITS1F", "ITS4"),
enzyme=c("BsuRI", "HpyCH4IV"))
knowns.data$size <- runif(nrow(knowns.data), min=40, max=800)
## Construct the TRAMPknowns object:[＃构造的TRAMPknowns对象：]
demo.knowns <- TRAMPknowns(knowns.data, knowns.info, warn.factors=FALSE)
## A plot of the pretend knowns:[＃A图的装作已知：]
plot(demo.knowns, cex=1, group.clusters=TRUE)
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 2012-10-1 11:44:32
