R语言估计单细胞数据中的噪声。write_noise_model()函数-中英文对照帮助文档
By MicroRbt Martinez PhD
R语言函数名：write_noise_model()
R语言函数功能：估计单细胞数据中的噪声。
来自资源库：Bionconductor-software
write_noise_model()函数所属R语言包：所在R包具体名称、包功能的中英文双语描述见正文后面'--所在R语言包信息--'部分。
描述-----Description-----
Estimates the drop-out model and technical variance from spike-ins present in the sample.
根据样本中存在的尖峰估计退出模型和技术差异。
使用方法-----Usage-----
estimate_noiseparameters(SCEList, plot=FALSE, sd_inflate=0, max_cumprob=0.9999,
bins=10, write.noise.model=TRUE, file="noise_estimation",
dropout_inflate=1, model_view=c("Observed", "Optimized"),
alpha_resolution=0.005, tie_function="maximum")
参数-----Arguments-----
参数SCEList介绍: A SingleCellExperiment object that must contain the observed counts matrix as "observed_expression" in assays, and must have the relevant spike-in samples identified using isSpike() as well as contain the expected actual concentrations of these spike-ins as spikeConcentrations in metadata. Please see the vignette for more detail about constructing the appropriate SCEList.
一个SingleCellExperiment对象，必须包含在assays中观察到的计数矩阵为"observed_expression"，并且必须具有使用isSpike()标识的相关加标样本，并且包含这些加标的预期实际浓度为[[ metadata中的spikeConcentrations。请参阅插图，以获取有关构建适当的SCEList的更多详细信息。
参数plot介绍: When plot=TRUE produces plots to investigate quality of data fits with root file name set by file option.
当plot=TRUE生成图来调查数据质量时，其根文件名由file选项设置。
参数sd_inflate介绍: An optional parameter to modulate the estimated noise. The estimated standard deviation of spike-ins can be scaled by this factor. We recommend leaving the value at the default of 0.
可选参数，用于调制估计的噪声。尖峰信号的估计标准偏差可以通过此因子进行缩放。我们建议将该值保留为默认值0。
参数bins介绍: The parameter determines the number of bins for comparison of the quality of fit between the mixed-model and observed data for each spike-in alpha in order to calculate the relationship between alpha and mean in the noise model. This should be set lower for small datasets and higher for datasets with more observations
该参数确定用于比较混合模型与每个尖峰α的观测数据之间的拟合质量的仓数，以便计算噪声模型中的alpha与均值之间的关系。对于小型数据集，应将其设置为较低；对于具有更多观测值的数据集，应将其设置为较高
参数max_cumprob介绍: Because a cumulative distribution will range from n=0 to a countable infinity, the event space needs to be set to cover a reasonable fraction of the probability density. This parameter determines the the fraction of probability density covered by the event space, which in turn defines the highes count number in the event space. We recommend users use the default value of 0.9999.
因为累积分布的范围是从n = 0到可数的无穷大，所以需要将事件空间设置为覆盖合理比例的概率密度。此参数确定事件空间所覆盖的概率密度的分数，而分数又定义了事件空间中的高计数数。我们建议用户使用默认值0.9999。
参数write.noise.model介绍: When write.noise.model=TRUE outputs two tab-delimited files containing the dropout effects and noise model parameters; this allows users to apply the noise generation on a seperate high compute node. The root file name is set by file option.
当write.noise
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发表于 2021-2-20 02:52:01
