relativeCN(Repitools)
relativeCN()所属R语言包：Repitools
Calculate and Segment Relative Copy Number From Sequencing Counts
从测序计数计算和分部的相对拷贝数
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function uses the GCadjustCopy function to convert a matrix of count data into absolute copy number estimates, then calculates the log2 fold change ratio and segments these values.
此功能使用GCadjustCopy函数计数数据矩阵转换成绝对拷贝数的估计，然后计算的log2倍的变化率和细分这些值。
用法----------Usage----------
## S4 method for signature 'data.frame,matrix'
relativeCN(input.windows, input.counts, gc.params = NULL,
..., verbose = TRUE)
## S4 method for signature 'GRanges,matrix'
relativeCN(input.windows, input.counts, gc.params = NULL,
..., 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. The first column must be for the control state, and the second column must be for the treatment state.
一个矩阵的计数。第一列必须为控制状态，而第二列必须是用于治疗状态。
参数：gc.params
A GCAdjustParams object, holding parameters related to mappability and GC content correction of read counts, or NULL, if GC content correction is not desired.
一个GCAdjustParams对象，持有涉及到mappability和读取计数，或NULL GC含量校正的参数，如果GC含量校正不理想。
参数：...
Further parameters passed to segment function in DNAcopy package, and also the segment.sqrt parameter to absoluteCN.
进一步的参数传递给segmentDNAcopy包，也是segment.sqrt参数absoluteCN，功能。
参数：verbose
Whether to print the progess of processing.
无论是打印处理陆侃。
Details
详情----------Details----------
The algorithm used to call the copy number regions is Circular Binary Segmentation (Olshen et al. 2004). Weights for each window, that are the inverse of the variance, calculated with the delta method, are always used. Windows or regions that were not in the segmentation result are given the value NA.
调用拷贝数的区域使用的算法是循环二元分割（Olshen等，2004）。每个窗口的重量，是方差与Delta方法计算，逆，始终使用。 Windows或区域分割结果不给出价值NA。
If gc.params is NULL, then no correction for mappability or GC content is done. This can be done when the bias in both treatment and control samples is assumed to be equal. If gc.params is specified, then absolute copy numbers are estimated with GCadjustCopy for each condition, which corrects for mappability and then GC content, before estimating absolute copy numbers. The ratio of estimated absolute copy numbers is segmented, to calculate relative copy numbers.
如果gc.params是NULL，则无须更正为mappability或GC含量做了。这可以被认为是治疗和控制样本偏差平等。如果gc.params被指定，那么绝对拷贝数估计GCadjustCopy每个条件，其中纠正mappability然后GC含量估计绝对拷贝数。估计绝对拷贝数的比例分割，计算相对拷贝数。
值----------Value----------
If gc.params was given, then a AdjustedCopyEstimate object. Otherwise, a CopyEstimate object. The copy number ratios are on the linear scale, not log2.
如果gc.params给AdjustedCopyEstimate对象。否则，一个CopyEstimate对象。拷贝数比率线性度，而不是的log2。
作者（S）----------Author(s)----------
Dario Strbenac
参考文献----------References----------
Circular binary segmentation for the analysis of array-based DNA copy number data.
举例----------Examples----------
inputs <- data.frame(chr = c("chr1", "chr1", "chr1", "chr2", "chr2"),
start = c(1, 50001, 100001, 1, 10001),
end = c(50000, 100000, 150000, 10000, 20000))
counts <- matrix(c(25, 39, 3, 10, 22, 29, 38, 5, 19, 31), nrow = 5)
colnames(counts) <- c("Control", "Treatment")
relativeCN(inputs, input.counts = counts, p.method = "perm")
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 12:52:00
