normalizeTumorBoost.numeric(aroma.light)
normalizeTumorBoost.numeric()所属R语言包：aroma.light
Normalizes allele B fractions for a tumor given a match normal
肿瘤规范化等位基因B组分给予匹配正常
译者：生物统计家园网 机器人LoveR
描述----------Description----------
TumorBoost [1] is a normalization method that normalizes the allele B fractions of a tumor sample given the allele B fractions and genotypes of a matched normal. The method is a single-sample (single-pair) method. It does not require total copy-number estimates. The normalization is done such that the total copy number is unchanged afterwards.
TumorBoost [1]是一个标准化标准化肿瘤样本的等位基因B组分B等位基因匹配的正常分数和基因型的方法。该方法是一个单一的样本（单对）方法。它不需要总拷贝数的估计。标准化等，总拷贝数是不变的，后来做了。
用法----------Usage----------
参数----------Arguments----------
参数：betaT, betaN
Two numeric vectors each of length J with tumor and normal allele B fractions, respectively.
两个numericvector的每个长度为j的肿瘤和正常的等位基因B组分，分别。
参数：muN
An optional vector of length J containing normal genotypes calls in (0,1/2,1,NA) for (AA,AB,BB).
一个可选的vector长度为j呼吁含有正常基因型（0,1 / 2,1，NA）（AA，AB和BB）。
参数：flavor
A character string specifying the type of correction applied.
一个character字符串指定类型的校正应用。
参数：preserveScale
If TRUE, SNPs that are heterozygous in the matched normal are corrected for signal compression using an estimate of signal compression based on the amount of correction performed by TumorBoost on SNPs that are homozygous in the matched normal.
如果TRUE，这是相匹配的正常的杂合子的单核苷酸多态性纠正使用的基础上的单核苷酸多态性，是相匹配的正常纯合子由TumorBoost进行校正量估计信号压缩为信号压缩。
参数：...
Argument passed to callNaiveGenotypes(), if called.
参数传递callNaiveGenotypes（），如果调用。
Details
详情----------Details----------
Allele B fractions are defined as the ratio between the allele B signal and the sum of both (all) allele signals at the same locus. Allele B fractions are typically within [0,1], but may have a slightly wider support due to for instance negative noise. This is typically also the case for the returned normalized allele B fractions.
等位基因B信号都在相同的轨迹（全部）等位基因信号的总和之间的比率被定义为等位基因B组分。 B等位基因分数通常在[0,1]，但可能由于负面噪音例如一个稍微更广泛的支持。这通常是返回归等位基因B组分的情况下。
值----------Value----------
Returns a numeric vector of length J containing the normalized allele B fractions for the tumor. Attribute modelFit is a list containing model fit parameters.
返回numericvector长度为j的等位基因为B的肿瘤规范化分数。属性modelFit是list含模型拟合参数。
口味----------Flavors----------
This method provides a few different "flavors" for normalizing the data. The following values of argument flavor are accepted:
这种方法提供了几个不同的“口味”数据标准化。参数flavor以下值接受：
v4: (default) The TumorBoost method, i.e. Eqns. (8)-(9) in [1].
V4：（默认）TumorBoost方法，即Eqns。 （8） - [1]（9）。
v3: Eqn (9) in [1] is applied to both heterozygous and homozygous SNPs, which effectly is v4 where the normalized allele B fractions for homozygous SNPs becomes 0 and 1.
V3：EQN [1]（9）杂合和纯合单核苷酸多态性，等位基因为纯合子的SNPs归乙分数变成0和1这effectly是V4。
v2: ...
V2：...
v1: TumorBoost where correction factor is force to one, i.e. η_j=1. As explained in [1], this is a suboptimal normalization method. See also the discussion in the paragraph following Eqn (12) in [1].
V1：TumorBoost校正因子的力量之一，即η_j=1。 [1]中的解释，这是一个最理想的标准化方法。也看到在后段的讨论式（12）[1]。
保规模----------Preserving scale----------
Allele B fractions are more or less compressed toward a half, e.g. the signals for homozygous SNPs are slightly away from zero and one. The TumorBoost method decreases the correlation in allele B fractions between the tumor and the normal conditioned on the genotype. What it does not control for is the mean level of the allele B fraction conditioned on the genotype.
B等位基因分数或多或少压缩走向了一半，如合子的SNPs的信号是稍微远离零和一。 TumorBoost方法降低等位基因B组分之间的肿瘤和正常空调基因型的相关性。它不控制什么条件B等位基因，基因型分数的平均水平。
By design, most flavors of the method will correct the homozygous SNPs such that their mean levels get close to the expected zero and one levels. However, the heterozygous SNPs will typically keep the same mean levels as before. One possibility is to adjust the signals such as the mean levels of the heterozygous SNPs relative to that of the homozygous SNPs is the same after as before the normalization.
根据设计，该方法最口味纠正合子的SNPs，他们的平均水平接近零和一的预期水平。然而，杂合子的SNPs通常保持和以前一样的平均水平。一种可能性是调整的信号，如杂合子的SNPs相对平均水平的纯合子的SNPs是相同的，后为前标准化。
If argument preserveScale=TRUE, then SNPs that are heterozygous (in the matched normal) are corrected for signal compression using an estimate of signal compression based on the amount of correction performed by TumorBoost on SNPs that are homozygous (in the matched normal).
如果参数preserveScale=TRUE，那么SNP是杂合子（在相匹配的正常）校正信号信号压缩的估计，基于的是纯合子由TumorBoost在SNP的校正量相匹配的正常使用压缩。
The option of preserving the scale is not discussed in the TumorBoost paper [1].
保持规模的选项是没有讨论的TumorBoost文献[1]。
作者（S）----------Author(s)----------
Henrik Bengtsson and Pierre Neuvial
参考文献----------References----------
TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays, BMC Bioinformatics, 2010, 11:245. [PMID 20462408]<br>
举例----------Examples----------
library(R.utils)
# Load data[加载数据]
pathname <- system.file("data-ex/TumorBoost,fracB,exampleData.Rbin", package="aroma.light")
data <- loadObject(pathname)
attachLocally(data)
pos <- position/1e6
muN <- genotypeN
layout(matrix(1:4, ncol=1))
par(mar=c(2.5,4,0.5,1)+0.1)
ylim <- c(-0.05, 1.05)
col <- rep("#999999", length(muN))[999999“，长度（门））]
col[muN == 1/2] <- "#000000"[000000“]
# Allele B fractions for the normal sample[正常样本的等位基因B组分]
plot(pos, betaN, col=col, ylim=ylim)
# Allele B fractions for the tumor sample[肿瘤样本的等位基因B组分]
plot(pos, betaT, col=col, ylim=ylim)
# TumorBoost w/ naive genotype calls[TumorBoost W /幼稚型分型]
betaTN <- normalizeTumorBoost(betaT=betaT, betaN=betaN)
plot(pos, betaTN, col=col, ylim=ylim)
# TumorBoost w/ external multi-sample genotype calls[TumorBoost W /外部多样品基因型呼吁]
betaTNx <- normalizeTumorBoost(betaT=betaT, betaN=betaN, muN=muN)
plot(pos, betaTNx, col=col, ylim=ylim)
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。
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发表于 2012-2-25 12:06:36
