在考虑到这种不同cell type proportion之间的相互依赖性之后,可以选用multivariate test的方式来检测那些cell type在healthy和disease sample中显著不同。 比如,Dirichlet-multinomial regression。 从multinomial distribution说起。 下面的数学公式和模型解释来源出处为:https://www.stat-center.pku.edu.cn/docs/2019022615081...
res = dirichlet_regression(counts, covariates, counts ~ condition)#ep.pvals = dirichlet_regression(counts=ep.freq, covariates=ep.cov, formula=counts ~ condition)$pvals# Calculate regressioncounts=as.data.frame(counts)counts$counts=DR_data(counts)data=cbind(counts,covariates)fit=DirichReg(counts~co...
首先我们先了解下 Dirichlet-multinomial regression 。 让我们从数学层面开始： 假设从正常组织取了sample i，正常组织本身包含了 p 种cell type，假设各种cell type出现的概率为 可能会相差很大，具有‘超散布性’ （overdispersion），也就是说观测到的不同样本中成分参数的方差会显著大于多项分布...
Previously, a Dirichlet–multinomial regression framework has been suggested to model this relationship, but it did not account for any underlying latent group structure. An underlying group structure of guts (such as enterotypes) has been observed across gut microbiome samples in which guts in the ...
监督学习里面稍微提了一下 multi-label 问题,解释了一下 MAP 估计(本书最常用的 inference),比较好奇的是 Google 的 SmartASS。后面是 regression,比较好奇的是某些书上倾向于称求解 为regression,而且这个似乎更说的通,比如按照这个书上的说法分类器 logistic regression 似乎是做分类的,但是名字里面可是有 ...
A generic random effects formulation for the Dirichlet negative multinomial distribution is developed together with a convenient regression parameterization. A simulation study indicates that, even when somewhat misspecified, regression models based on the Dirichlet negative multinomial distribution have smaller ...
regressioncluster samplingThe Dirichlet-multinomial model is considered as a model for cluster sampling. The model assumes that the design''s covariance matrix is a constant times the covariance under multinomial sampling. The use of this model requires estimating a parameter C, that measures the ...
For this, we describe a general class of hierarchical Dirichlet-multinomial regression models that use spike-and-slab priors for the selection of the significant associations. We further illustrate extensions that accommodate various parameterizations of a predictor's prior probability of inclusion and ...
Dirichlet multinomial regressionBACKGROUND. DNA methylation alterations have been found related to clear cell renal cell carcinoma (ccRCC). In addition, DNA methylation has been used to identify cell heterogeneity at the tumor level using cell deconvolution methods. Other cytosine modifications are less ...
Dirichlet-tree multinomial regressionMicrobiomeVariable selectionBackground: Understanding the relation between the human microbiome and modulating factors, such as diet, may help researchers design intervention strategies that promote and maintain healthy microbial communities. Numerous analytical tools are ...