Robust Tests for Differential Dispersion and Differential Expression in RNA-Sequencing Data

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Documentation for package ‘DiPhiSeq’ version 0.2.0

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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.