crlmmCopynumber(crlmm)
crlmmCopynumber()所属R语言包：crlmm
Locus- and allele-specific estimation of copy number
特定位点的等位基因拷贝数估计
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Locus- and allele-specific estimation of copy number.
轨迹和等位基因特异性拷贝数的估计。
用法----------Usage----------
crlmmCopynumber(object, MIN.SAMPLES=10, SNRMin = 5, MIN.OBS = 1,
DF.PRIOR = 50, bias.adj = FALSE,
prior.prob = rep(1/4, 4), seed = 1, verbose = TRUE,
GT.CONF.THR = 0.80, MIN.NU = 2^3, MIN.PHI = 2^3,
THR.NU.PHI = TRUE, type=c("SNP", "NP", "X.SNP", "X.NP"))
参数----------Arguments----------
参数：object
object of class CNSet.
对象类CNSet。
参数：MIN.SAMPLES
'Integer'. The minimum number of samples in a batch. Bathes with fewer than MIN.SAMPLES are skipped. Therefore, samples in batches with fewer than MIN.SAMPLES have NA's for the allele-specific copy number and NA's for the linear model parameters.
“整数”。最低数量在一个批次的样品。被跳过MIN.SAMPLES少浴室。因此，批次在比MIN.SAMPLES更少的样品具有的等位基因特异性拷贝数和线性模型参数NA NA。
参数：SNRMin
Samples with low signal to noise ratios are excluded.
低信号噪声比的样本被排除在外。
参数：MIN.OBS
For a SNP with with fewer than MIN.OBS of a genotype in a given batch, the within-genotype median is imputed. The imputation is based on a regression using SNPs for which all three biallelic genotypes are observed. For example, assume at at a given SNP genotypes AA and AB were observed and BB is an unobserved genotype. For SNPs in which all 3 genotypes were observed, we fit the model E(mean_BB) = beta0 + beta1*mean_AA + beta2*mean_AB, obtaining estimates; of beta0, beta1, and beta2. The imputed mean at the SNP with unobserved BB is then beta0hat + beta1hat * mean_AA of beta2hat * mean_AB.
为与较少比MIN.OBS在某一批次的基因型，基因型内的中位数是打杀的SNP。归集的基础上使用的SNPs为这所有三个等位基因基因型观察回归。例如，假设在一个特定的SNP基因型AA和AB公司进行了观察和BB是观测到的基因型。我们在所有观察到3种基因型的SNP，适合E型（mean_BB）= beta0 +β1的图* mean_AA + Beta2中* mean_AB，获得估计的beta0，β1和β2。估算平均的SNP与观测到的BB，然后beta0hat + beta1hat * mean_AA，对beta2hat * mean_AB。
参数：DF.PRIOR
The 2 x 2 covariance matrix of the background and signal variances is estimated from the data at each locus. This matrix is then smoothed towards a common matrix estimated from all of the loci. DF.PRIOR controls the amount of smoothing towards the common matrix, with higher values corresponding to greater smoothing. Currently, DF.PRIOR is not estimated from the data. Future versions may estimate DF.PRIOR empirically.
2×2的背景和信号方差协方差矩阵估计在每个位点的数据。对从所有的位点估计一个共同的矩阵，这个矩阵，然后平滑。 DF.PRIOR朝着共同的矩阵平滑，具有较高的价值相应的更大的平滑控制量。目前，DF.PRIOR是无法估计的数据。未来版本实证可能估计DF.PRIOR的。
参数：bias.adj
bias.adj is currently ignored (as well as the prior.prob argument). We plan to add this feature back to the crlmm package in the near future. This feature, when TRUE, updated initial estimates from the linear model after excluding samples with a low posterior probability of normal copy number. Excluding samples that have a low posterior probability can be helpful at loci in which a substantial fraction of the samples have a copy number alteration. For additional information, see Scharpf et al., 2010.
bias.adj是目前被忽略的（以及作为prior.prob参数）。我们计划在不久的将来的crlmm包添加此功能。此功能，当TRUE，更新线性模型的初步估计，扣除正常的拷贝数较低的后验概率样本。位点，其中相当一部分的样品有一个拷贝数改变可以帮助排除样品具有低的后验概率。如需详细资讯，请参阅Scharpf等。，2010。
参数：prior.prob
This argument is currently ignored. A numerical vector providing prior probabilities for copy number states corresponding to homozygous deletion, hemizygous deletion, normal copy number, and amplification, respectively.
这种说法目前被忽略。指出缺失，半合子缺失，正常的拷贝数，并放大，分别对应一个数值向量，提供拷贝数的先验概率。
参数：seed
Seed for random number generation.
随机数生成种子。
参数：verbose
Logical.
逻辑。
参数：GT.CONF.THR
Confidence threshold for genotype calls (0, 1). Calls with confidence scores below this theshold are not used to estimate the within-genotype medians. See Carvalho et al., 2007 for information regarding confidence scores of biallelic genotypes.
基因型分型（0，1）置信度阈值。呼吁低于这个theshold的信心分数不是用来估计内基因型的中位数。看到卡瓦略等人，2007等位基因基因型的信心分数的信息。
参数：MIN.NU
numeric. Minimum value for background intensity. Ignored if THR.NU.PHI is FALSE.
数字。背景强度的最低值。如果THR.NU.PHI是FALSE忽略。
参数：MIN.PHI
numeric. Minimum value for slope. Ignored if THR.NU.PHI is FALSE.
数字。斜坡的最低值。如果THR.NU.PHI是FALSE忽略。
参数：THR.NU.PHI
If THR.NU.PHI is FALSE, MIN.NU and MIN.PHI are ignored. When TRUE, background (nu) and slope (phi) coefficients below MIN.NU and MIN.PHI are set to MIN.NU and MIN.PHI, respectively.
如果THR.NU.PHI是FALSE，MIN.NU和MIN.PHI被忽略。当TRUE，背景（女）和坡度（PHI）低于MIN.NU和MIN.PHI系数设置到MIN.NU和MIN.PHI，分别。
参数：type
Character string vector that must be one or more of "SNP", "NP", "X.SNP", or "X.NP". Type refers to a set of markers. See details below
字符串向量，必须有一个或多个“单核苷酸多态性”，“NP”的，“X.SNP”，或“X.NP”。类型是指一组标记。下面详细说明
Details
详情----------Details----------
We suggest a minimum of 10 samples per batch for using crlmmCopynumber. 50 or more samples per batch is preferred and will improve the estimates.
我们建议使用crlmmCopynumber最低的10个批次样品。每批次样品50个或更多是首选，将改善的估计。
The functions crlmmCopynumberLD and crlmmCopynumber2 have been deprecated.
职能crlmmCopynumberLD和crlmmCopynumber2已被弃用。
The argument type can be used to specify a subset of markers for which the copy number estimation algorithm is run. One or more of the following possible entries are valid: 'SNP', 'NP', 'X.SNP', and 'X.NP'.
的说法type可以用来指定一个子集拷贝数估计算法运行的标记。一个或多个以下条目是有效的：“单核苷酸多态性”，“的NP，X.SNP，X.NP”。
'SNP' referers to autosomal SNPs.
“单核苷酸多态性”的email常染色体单核苷酸多态性。
'NP' refers to autosomal nonpolymorphic markers.
的NP“是指以常染色体显性遗传nonpolymorphic标记。
'X.SNP' refers to SNPs on chromosome X.
“X.SNP”是指X染色体上，以单核苷酸多态性
'X.NP' refers to autosomes on chromosome X.
“X.NP”是指在X染色体的染色体
However, users must run 'SNP' prior to running 'NP' and 'X.NP', or specify type = c('SNP', 'X.NP').
然而，用户必须执行“单核苷酸多态性”运行“的NP和X.NP之前，或指定type = c('SNP', 'X.NP')。
值----------Value----------
The value returned by the crlmmCopynumber function depends on whether the data is stored in RAM or whether the data is stored on disk using the R package ff for reading / writing. If uncertain, the first line of the show method defined for CNSet objects prints whether the assayData elements are derived from the ff package in the first line. Specifically,
crlmmCopynumber函数返回的值取决于数据是否存储在RAM或使用的R包ff读/写数据是否存储在磁盘上。如果不确定，show方法的第一行CNSet对象assayData包ff元素是否是从派生打印在第一线的定义。具体来说，
- if the elements of the batchStaticts slot in the CNSet object have the class "ff_matrix" or "ffdf", then the crlmmCopynumber function updates the data stored on disk and returns the value TRUE.
- 如果batchStaticts插槽的在CNSet对象中元素类“ff_matrix”或“ffdf”，然后crlmmCopynumber功能更新磁盘上的存储和数据传回值TRUE。
- if the elements of the batchStatistics slot in the CNSet object have the class 'matrix', then the crlmmCopynumber function returns an object of class CNSet with the elements of batchStatistics updated.
- 如果batchStatistics插槽要素在CNSet对象中有类矩阵，然后crlmmCopynumber函数返回一个类的对象CNSet的元素batchStatistics更新。
作者（S）----------Author(s)----------
R. Scharpf
参考文献----------References----------
normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics. 2007 Apr;8(2):485-99. Epub 2006 Dec 22. PMID: 17189563.
Quantifying uncertainty in genotype calls. Bioinformatics. 2010 Jan 15;26(2):242-9.
Irizarry RA, Biostatistics. Biostatistics, Epub July 2010.
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。
|
发表于 2012-2-25 16:02:48
