Man pages for syspremed/exploBATCH
Explore batch effect (exploBATCH) is a package for discovering and correcting for batch effect using an approach in Nyamundanda et al (2017).
| Aitkenf | Function for assessing model convergence |
| assessComBat | Assessing ComBat corrected data |
| assessCorrectBATCH | Assessing data corrected for batch effect using correctBATCH. |
| batchBreast | A vector identifying batches in the breast dataset. |
| batchColon | A vector identifying batches in the colon dataset. |
| bioCL | A vector identifying tumor and normal samples in the colon... |
| chol.inv | Matrix inversion |
| correctBatch | Batch correction approach based on the PPCCA model. |
| correctComBat | Batch correction with ComBat |
| emQ | EM algorithm for PPCA model. |
| expBATCH | Discovering and correcting batch effect. |
| exploBATCH-package | Explore batch effect (exploBATCH) is a package for... |
| findBATCH | A function to formally tests presence of batch effect. |
| iniA | Function for initializing regression on the LVs. |
| jEM | EM algorithm for PPCCA model jackkniifing. |
| mdiag | Sum diagonal elements of a matrix |
| pcaBeforeCorrection | PCA before correction. |
| pen | Penalty term for BIC |
| ppcca | Fitting PPCCA model |
| ppccaBeforeCorrection | PPCCA before correction. |
| ppccajack | Fitting PPCCA model with jackknifing |
| rcpparma_hello_world | Set of functions in example RcppArmadillo package |
| rowVar | Row variance |
| scalingfn | Scaling of data |
| standardize | Function for standardizing covariates |
| unlistfn | Unlist an lapply function |
