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 |

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