GCadjustCopy(Repitools)
GCadjustCopy()所属R语言包：Repitools
Calculate Absolute Copy Number from Sequencing Counts
计算从测序计数的绝对拷贝数
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Taking into account mappability and GC content biases, the absolute copy number is calculated, by assuming that the median read depth is a copy number of 1.
考虑到的帐户mappability和GC含量偏见，绝对拷贝数的计算，假设中位数的阅读深度为1拷贝数。
用法----------Usage----------
## S4 method for signature 'data.frame,matrix,GCAdjustParams'
GCadjustCopy(input.windows, input.counts,
gc.params, ...)
## S4 method for signature 'GRanges,matrix,GCAdjustParams'
GCadjustCopy(input.windows, input.counts,
gc.params, verbose = TRUE)
参数----------Arguments----------
参数：input.windows
A data.frame with (at least) columns chr, start, and end, or a GRanges object.
一个data.frame（至少）列chr，start，end，或农庄对象。
参数：input.counts
A matrix of counts. Rows are genomic windows and columns are samples.
一个矩阵的计数。行基因组窗口和列样品。
参数：gc.params
A GCAdjustParams object, holding parameters related to mappability and GC content correction of read counts.
一个GCAdjustParams对象，持有涉及到mappability和读取计数的GC含量校正参数。
参数：...
verbose argument, if data.frame method called.
verbose的说法，如果data.frame方法调用。
参数：verbose
Whether to print the progess of processing.
无论是打印处理陆侃。
Details
详情----------Details----------
First, the mappability of all counting windows is calculated, and windows that have mappability less than the cutoff specified by in the parameters object are ignored in further steps. The remaining windows have their counts scaled by multiplying their counts by 100 / percentage mappability.
首先，计算所有点票窗口mappability，窗口，有mappability小于参数对象在指定的截止忽略进一步的步骤。其余窗口的比例乘以100 /百分比mappability计数的计数。
The range of GC content of the counting windows is broken into a number of bins, as specified by the user in the parameters object. A probability density function is fitted to the counts in each bin, so the mode can be found. The mode is taken to be the counts of the copy neutral windows, for that GC content bin.
成箱的数量，由用户在参数对象指定票窗口GC含量范围被打破。概率密度函数是装在每个容器计数，因此可以发现模式。采取的模式是副本中立窗口计数，GC含量斌。
A polynomial function is fitted to the modes of GC content bins. Each count is divided by its expected counts from the polynomial function to give an absolute copy number estimate. If the ploidy has been provided in the parameters object, then all counts within a sample are multiplied by the ploidy for that sample. If the sample ploidys were omitted, then no scaling for ploidy is done.
多项式函数拟合GC含量箱模式。每个数除以它预计从多项式函数给出一个绝对的拷贝数的估计数。如果参数中的对象提供的套数已，然后在所有样品计数乘以该样本的套数。如果样品ploidys被省略，则没有套数缩放完成。
值----------Value----------
A AdjustedCopyEstimate object describing the input windows and their estimates.
一个AdjustedCopyEstimate对象描述的输入窗口和他们的估计。
作者（S）----------Author(s)----------
Dario Strbenac
举例----------Examples----------
## Not run: [＃无法运行：]
library(BSgenome.Hsapiens.UCSC.hg18)
library(BSgenome.Hsapiens36bp.UCSC.hg18mappability)
load("inputsReads.RData")
windows <- genomeBlocks(Hsapiens, chrs = paste("chr", c(1:22, 'X', 'Y'), sep = ''),
width = 20000)
counts <- annotationBlocksCounts(inputsReads, anno = windows, seq.len = 300)
gc.par <- GCAdjustParams(genome = Hsapiens, mappability = Hsapiens36bp,
min.mappability = 50, n.bins = 10, min.bin.size = 10,
poly.degree = 4, ploidy = c(2, 4))
abs.cn <- GCadjustCopy(input.windows = windows, input.counts = counts, gc.params = gc.par)
## 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 2012-2-26 12:49:56
