diphiseq |
Main function. For most users, this function is all what they need for the analysis. |

example_data |
Numeric count matrix of example data. |

outprop |
Give a rough estimate of the proportion of outliers in the data based on the results of DiPhiSeq. |

robnb |
Calculates the estimate and standard error of beta and phi. It takes as input counts from one group of samples for a single gene. This function is the core underlining function of the whole package. A significant part of the code is edited based on William H. Aeberhard's glmrob.nb R function; we appreciate them very much for sharing their code online. This function also implement Algorithm 1 of our submitted paper about DiPhiSeq. This function is called by robtest. Most users don't need to call this function directly. |

robtest |
Calls the robnb function to estimate the coefficients, and then construct the statistical tests for DD and DE. It works for a single gene. y1 and y2 are count vectors for a single gene. diphiseq calls this function to do the calculation for each gene. Normal users often don't need to use this function directly. |