DGEobj.utils-package |
DGEobj.utils Package Overview |

convertCounts |
Convert count matrix to CPM, FPKM, FPK, or TPM |

extractCol |
Extract a named column from a series of df or matrices |

lowIntFilter |
Apply low intensity filters to a DGEobj |

rsqCalc |
Calculate R-squared for each gene fit |

runContrasts |
Build contrast matrix and calculate contrast fits |

runEdgeRNorm |
Run edgeR normalization on DGEobj |

runIHW |
Apply Independent Hypothesis Weighting (IHW) to a list of topTable dataframes |

runPower |
Run a power analysis on counts and design matrix |

runQvalue |
Calculate and add q-value and lFDR to dataframe |

runSVA |
Test for surrogate variables |

runVoom |
Run functions in a typical voom/lmFit workflow |

summarizeSigCounts |
Summarize a contrast list |

topTable.merge |
Merge specified topTable df cols |

tpm.direct |
Convert countsMatrix and geneLength to TPM units |

tpm.on.subset |
Calculate TPM for a subsetted DGEobj |