simChIP(ChIPsim)
simChIP()所属R语言包：ChIPsim
Simulate ChIP-seq experiments
模拟芯片跳台实验
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function acts as driver for the simulation. It takes all required arguments and passes them on to the functions for the different stages of the simulation. The current defaults will simulate a nucleosome positioning experiment.
此功能作为驱动的模拟。它需要所有必需的参数，并将它们传递到模拟不同阶段的功能。当前的默认值将模拟核小体定位实验。
用法----------Usage----------
simChIP(nreads, genome, file, functions = defaultFunctions(),
control = defaultControl(), verbose = TRUE, load = FALSE)
参数----------Arguments----------
参数：nreads
Number of reads to generate.
读取数生成。
参数：genome
An object of class 'DNAStringSet' or the name of a fasta file containing the genome sequence.
一个对象类的“DNAStringSet”或一个FASTA文件中包含的基因组序列的名称。
参数：file
Base of output file names (see Details).
相应的输出文件的名称（见详情）。
参数：functions
Named list of functions to use for various stages of the simulation, expected names are: "features", "bindDens", "readDens", "sampleReads", "readNames", "readSequence"
功能用于模拟的各个阶段，预计名称命名的列表是：功能，bindDens，readDens，sampleReads“，”readNames，readSequence
参数：control
Named list of arguments to be passed to simulation functions (one list per function).
命名参数列表被传递到模拟功能（每一个功能列表）。
参数：verbose
Logical indicating whether progress messages should be printed.
逻辑说明是否应打印进度消息。
参数：load
Logical indicating whether an attempt should be made to load intermediate results from a previous run.
逻辑指示是否应该尝试加载之前运行的中间结果。
Details
详情----------Details----------
The simulation consists of six of stages:
模拟包括六个阶段：
generate feature sequence (for each chromosome): chromosome length -> feature sequence (list)
生成特征序列（每个染色体）：染色体长度 - >功能顺序（名单）
compute binding site density: feature sequence -> binding site density (vector)
计算结合位点密度：特征序列 - >结合位点的密度（矢量）
compute read density: binding site density -> read density (two column matrix, one column for each strand)
计算密度：结合位点密度读 - >读密度（两列的矩阵，每一条链的一列）
sample read start sites: read density -> read positions (list)
样品读取起始位点：读密度 - >读仓（名单）
create read names: number of reads -> unique names
创建读的名字：读取数 - >独特的名字
obtain read sequence and quality: read positions, genome sequence, [qualities] -> output file
获得读序列和质量：读取位置，基因组序列，[品质] - >输出文件
After each of the first three stages the results of the stage are written to a file and can be reused later. File names are created by appending "_features.rdata", "_bindDensity.rdata" and "_readDensity.rdata" to file respectively. Previous results will be loaded for reuse if load is TRUE and files with matching names are found. This is useful to sample repeatedly from the same read density or to recover partial results from an interrupted run.
后的前三个阶段，每个阶段的结果将被写入到一个文件，以后可以重复使用。文件名加上_features.rdata，_bindDensity.rdata创建_readDensity.rdatafile分别。重用以前的结果将被载入，如果load是TRUE与名称匹配的文件被发现。品尝反复读密度相同或恢复中断运行的部分结果，这是非常有用的。
The creation of files can be prevented by setting file = “”. In this case all results will be returned in a list at the end. Note that this will require more memory since all intermediate results have to be held until the end.
文件的创建，是可以预防的设置file = “。在这种情况下，所有的结果将返回列表中结束。请注意，这将需要更多的内存，因为所有的中间结果，直到年底举行。
The behaviour of the simulation is mainly controlled through the functions and control arguments. They are expected to be lists of the same length with matching names. The names indicate the stage of the simulation for which the function should be used; elements of control will be used as arguments for the corresponding functions.
模拟的行为主要控制通过functions和control的参数。他们预计将是相同的长度相匹配的名字列表。的名称表明了模拟的阶段，应使用的功能;元素control将使用相应的功能参数。
值----------Value----------
A list. The components are typically either lists (with one component per chromosome) or file names but note that this may depend on the return value of functions listed in functions. The components of the returned list are:
一个列表。这些组件通常是要么列表（每个染色体的一个组成部分）或文件名，但要注意，这可能取决于在functions列出的函数的返回值。返回列表中的组件是：
参数：features
Either a list of generated features or the name of a file containing that list;
无论是产生的功能或包含该列表的文件名列表;
参数：bindDensity
Either a list with binding site densities or the name of a file containing that list;
无论是与结合位点密度或包含该列表的文件名列表;
参数：readDensity
Either a list of read densities or the name of a file containing that list;
无论是读取密度或包含该列表的文件名列表;
参数：readPosition
Either a list of read start sites or the name of a file containing that list;
无论是读起始位点或包含该列表的文件名列表;
参数：readSequence
The return value of the function listed as "readSequence". The default for this the name of the fastq file containing the read sequences;
readSequence中列出的函数的返回值。默认包含读取序列的fastq文件的名称;
参数：readNames
Either a list of read names or the name of a file containing that list.
无论是只读的名称或包含该列表的文件名列表。
作者（S）----------Author(s)----------
Peter Humburg
参见----------See Also----------
defaultFunctions, defaultControl
defaultFunctions，defaultControl
举例----------Examples----------
## Not run: [＃无法运行：]
## To run the default nucleosome positioning simulation [＃要运行的默认的核小体定位模拟]
## we can simply run something like the line below.[＃我们可以简单地运行下面的像行。]
## This will result in 10 million reads sampled from the genome.[＃这将导致10万美元从基因组的采样读取。]
## Of course the file names have to be changed as appropriate. [＃当然，文件名必须加以适当的改变。]
simChIP(1e7, genome = "reference.fasta", file = "output/sim_10M")
## End(Not run)[＃结束（不运行）]
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 2012-2-25 14:57:36
