Man pages for lunge111/intSEQ
Differential Expression Analysis of RNA-seq Data with Integrated Likelihood Method
| condition | The conditions of Mont&pick data |
| count.data | The count table of Montgomery and Pickrell data. |
| edgeR.QL.running | Implement Quasi likelihood method by default settings. |
| Hessian | Hessian matrix with respect to the dispersion. |
| intSEQ | Implement integrated likelihood ratio test. |
| intSEQ-package | Differential Analysis of RNA-seq Data with Integrated... |
| joint.like | Calculate the joint likelihood |
| joint.likelihood | Calculate the joint likelihood of a vector of dispersion. |
| likelihoodpercond | The likelihood in each group. |
| limma.trans.running | Transformation method with limma. |
| limma.voom.running | Implement voom with limma by default settings. |
| marginal.LR | Calculate the integrated likelihood ratio. |
| mednorm | Median normalization method for limma trans. |
| NBsimu | Generate synthetic RNA-seq data. |
| pcut | Calculate the proportion of rejections for given levels. |
| plotComp | Plot the simulation comparison results. |
| ran.nb | Generate negative binomial random samples. |
| ran.poi | Generate Poisson random sample. |
| sample.nb | Generate negative binomial count table random sample. |
| show | Show the result of 'intSEQ' |
| simuComp | Simulation for the four methods and compare the p value. |
| summary | Summary of comparison results. |
| tran1 | The transformation function of limma.trans. |
| tran.est | Estimate the coefficient in limma trans. |
| tran.reg | The regression part of limma trans. |
