computeCoverage(Genominator)
computeCoverage()所属R语言包：Genominator
Compute effort-coverage values
计算覆盖率的努力值
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Compute fraction coverage obtained for a certain degree of sequencing effort.
计算分数的覆盖面得到一定程度的测序努力。
用法----------Usage----------
computeCoverage(expData, annoData,
cutoff = function(x, anno, group) { x > 10 },
effort = seq(1e+05, 5e+07, length = 20),
smooth = function(probs) { probs },
groups = rep("ALL", length(what)),
what = getColnames(expData, all = FALSE),
totals = summarizeExpData(expData, what = what, verbose = verbose),
ignoreStrand = FALSE, verbose = getOption("verbose"), ...)
参数----------Arguments----------
参数：expData
An ExpData object.
ExpData对象。
参数：annoData
A data frame which must contain the columns chr, start, end and strand which specifies annotation regions of interest.
一个数据框，其中必须包含列chr，start，end和strand指定利益注释区域。
参数：cutoff
A predicate which determines when a region of annotation has been "sequenced". This function takes three arguments x = number of reads in region, anno = the annotation description of the region, group = the group it is in.
决定一个区域的注释时已测序的谓词“。这个函数需要三个参数，X =读取数量在区域，ANNO =该区域的注释说明，组=组所在
参数：effort
Effort is a vector of how much sequencing has been done.
努力是向量的多少排序已经完成。
参数：smooth
A function which takes as input the vector of probabilities and must return the probabilities.
作为输入的概率向量和函数必须返回的可能性。
参数：groups
The different groups for which to calculate coverage.
为不同的群体来计算覆盖率。
参数：what
The different columns, must be the same length as the groups.
不同的列，必须作为群体的长度相同。
参数：totals
The lane totals, or some other totals. This allows us to estimate the sampling probability vector.
车道总数，或一些其他的总数。这使我们能够估计的抽样概率向量。
参数：ignoreStrand
Whether or not to add over strands.
是否添加过股。
参数：verbose
Do you want to see output.
你想看到输出。
参数：...
Extra argument passed to cutoff.
额外的参数传递到截止。
Details
详情----------Details----------
This argument is pretty general as different ways of specifying the arguments allows one to compute "coverage" under a lot of different definitions.
作为指定参数的方式不同，这种说法是相当普遍的，允许一个计算“覆盖”下了很多不同的定义。
值----------Value----------
Returns an object of class genominator.coverage. Pretty much you'll want to call plot on this object.
类genominator.coverage返回一个对象。几乎你想对这个对象调用的图。
作者（S）----------Author(s)----------
James Bullard <a href="mailto:bullard@berkeley.edu">bullard@berkeley.edu</a>, Kasper Daniel
Hansen <a href="mailto:khansen@jhsph.edu">khansen@jhsph.edu</a>
参见----------See Also----------
See the plot.genominator.coverage for the plotting method and the Genominator vignette for details.
见绘制方法和plot.genominator.coverage细节暗角Genominator。
举例----------Examples----------
ed <- ExpData(system.file(package = "Genominator", "sample.db"),
tablename = "raw")
data("yeastAnno")
a <- computeCoverage(ed, yeastAnno, effort = 2^(5:18),
cutoff = function(x, ...) x > 1, smooth = FALSE)
names(a)
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 19:31:11
