syntheticNucMap(nucleR)
syntheticNucMap()所属R语言包：nucleR
Generates a synthetic nucleosome map
生成一个合成的核小体图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function generates a synthetic nucleosome map using the parameters given by the user and returns the coverage (like NGS experiments) or a pseudo-hybdridization ratio (like Tiling Arrays) toghether with the perfect information about the well positioned and fuzzy nucleosome positions.
这个函数生成一个核小体的合成图，使用由用户给定的参数和返回的覆盖面（如农工商实验）或伪hybdridization比率（如平铺阵列）与核小体的位置以及定位和模糊完善的信息toghether的。
用法----------Usage----------
syntheticNucMap(wp.num=100, wp.del=10, wp.var=20, fuz.num=50, fuz.var=50, max.cover=20, nuc.len=147, lin.len=20, rnd.seed=NULL, as.ratio=FALSE, show.plot=FALSE, ...)
参数----------Arguments----------
参数：wp.num
Number of well-positioned (non overlapped) nucleosomes. They are placed uniformly every nuc.len+lin.len basepairs.
定位（非重叠）核小体的数量。它们被放置均匀每nuc.len+lin.len碱基对。
参数：wp.del
Number of well-positioned nucleosomes (the ones generated by wp.num) to remove. This will create an uncovered region.
核小体定位（wp.num生成的）删除的数目。这将创建一个裸露区域。
参数：wp.var
Maximum variance in basepairs of the well-positioned nucleosomes. This will create some variation in the position of the reads describing the same nucleosome
最大定位核小体的碱基变异。这将创建一些变化，在描述相同的核小体读取的位置
参数：fuz.num
Number of fuzzy nucleosomes. They are distributed randomly over all the region. They could be overlapped with other well-positioned or fuzzy nucleosomes.
模糊核小体的数量。它们是随机分布的所有区域。他们可以与其他定位或模糊的核小体的重叠。
参数：fuz.var
Maximum variance of the fuzzy nucleosomes. This allow to set different variance in well-positioned and fuzzy nucleosome reads (using wp.var and fuz.var)
模糊核小体的最大差异。这允许设置不同的差异，在定位和模糊的核小体读取（使用wp.var和fuz.var）
参数：max.cover
Maximum coverage of a nucleosome, i.e., how many times a nucleosome read can be repeated. The final coverage probably will be higher by the addition of overlapping nucleosomes.
最大的核小体，即可以重复多少次核小体读覆盖。最终的覆盖面可能会是由重叠的核小体除了高。
参数：nuc.len
Nucleosome length. It's not recomended change the default 147bp value.
核小体的长度。它不是recomended改变默认147bp值。
参数：lin.len
Linker DNA length. Usually around 20 bp.
连接器的DNA长度。一般约20基点。
参数：rnd.seed
As this model uses random distributions for the placement, by setting the rnd.seed to a known value allows to reproduce maps in different executions or computers. If you don't need this, just left it in default value.
由于这种模式采用随机分布的位置，允许在不同的处决或计算机重现图，通过设置一个已知值的rnd.seed。如果你不需要这个，刚刚离开它在默认值。
参数：as.ratio
If as.ratio=TRUE this will create and return a synthetic naked DNA control map and the ratio between it and the nucleosome coverage. This can be used to simulate hybridization ratio data, like the one in Tiling Arrays.
如果as.ratio=TRUE这将创建并返回一种人工合成的裸DNA控制图和它与核小体覆盖的比例。这可以用来模拟杂交率数据，如在一个平铺阵列。
参数：show.plot
If TRUE, will plot the output coverage map, with the nucleosome calls and optionally the calculated ratio.
如果TRUE，将绘制出覆盖图，与核小体的通话和选择性的比例计算。
参数：...
Additional parameters to be passed to plot if show.plot=TRUE
额外的参数被传递到plot如果show.plot=TRUE
值----------Value----------
A list with the following elements:
具有下列内容的列表：
参数：wp.starts
Start points of well-positioned nucleosomes
定位核小体的启动点
参数：wp.nreads
Number of repetitions of each well positioned read
每口井的位置读取的重复数
参数：wp.reads
Well positioned nucleosome reads (IRanges format), containing the repetitions
以及定位核小体读取（IRanges格式），包含重复
参数：fuz.starts
Start points of the fuzzy nucleosomes
模糊核小体的启动点
参数：fuz.nreads
Number of repetitions of each fuzzy nucleosome read
读取的每一个模糊的核小体的重复数
参数：fuz.reads
Fuzzy nucleosome reads (IRanges format), containing all the repetitions
模糊核小体读取（IRanges格式），包含了所有的重复
参数：syn.reads
All synthetic nucleosome reads togheter (IRanges format)
所有合成的核小体读取togheter（IRanges格式）
The following elements will be only returned if as.ratio=TRUE:
下列元素将只返回，如果as.ratio=TRUE：
参数：ctr.reads
The pseudo-naked DNA (control) reads (IRanges format)
伪裸DNA（对照组）读（IRanges格式）
参数：syn.ratio
The calculated ratio nucleosomal/control (Rle format)
核小体/控制（Rle格式计算的比例）
作者（S）----------Author(s)----------
Oscar Flores <a href="mailto flores@mmb.pcb.ub.es">oflores@mmb.pcb.ub.es</a>
举例----------Examples----------
#Generate a synthetic map with 50wp + 20fuzzy nucleosomes using fixed random seed=1[生成一个使用固定随机种子= 1 + 20fuzzy 50wp核小体的合成图]
res = syntheticNucMap(wp.num=50, fuz.num=20, show.plot=TRUE, rnd.seed=1)
#Increase the fuzzyness[增加的fuzzyness]
res = syntheticNucMap(wp.num=50, fuz.num=20, wp.var=70, fuz.var=150, show.plot=TRUE, rnd.seed=1)
#Calculate also a random map and get the ratio between random and nucleosomal[计算也是一个随机图，随机和核小体之间的比例]
res = syntheticNucMap(wp.num=50, wp.del=0, fuz.num=20, as.ratio=TRUE, show.plot=TRUE, rnd.seed=1)
print(res)
#Different reads can be accessed separately from results[不同的读分别从结果可以访问]
#Let's use this to plot the nucleosomal + the random map[让使用这个绘制的核小体+随机图]
par(mfrow=c(3,1), mar=c(3,4,1,1))
plot(as.vector(coverage(res$syn.reads)), type="h", col="red", ylab="nucleosomal", ylim=c(0,35))
plot(as.vector(coverage(res$ctr.reads)), type="h", col="blue", ylab="random", ylim=c(0,35))
plot(as.vector(res$syn.ratio), type="h", col="orange", ylab="ratio")
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 2012-2-26 07:55:57
