getBCVTable: Get a table of genewise BCV values from a DGEList

In DarwinAwardWinner/rctutils: Utility functions by Ryan C. Thompson

Get a table of genewise BCV values from a DGEList

Description

Given a DGEList object, this will extract the average logCPM as well as the common, trended, and genewise dispersion values. In addition, it will re-estimate the dispersions with no empirical Bayes shrinkage (prior.df = 0) to obtain the raw genewise dispersion values.

Usage

getBCVTable(y, design, ..., rawdisp)

Arguments

y	A DGEList. If it does not already contain dispersion values, they will be estimated.
design	A design matrix to use when estimating dispersions. This is optional if y already contains a design.
...	Additional arguments are passed to edgeR::estimateDisp(), if dispersion estimation is required (see below).
rawdisp	Another DGEList, which should be identical to y except that it had dispersions estimated with prior.count = 0. This argument is completely optional, and is only used for speeding up the function if the raw dispersions have already been estimated. To suppress estimation of raw dispersions entirely, set this to NA, NULL, or FALSE. (TODO: Take a long hard look at the logic in this function and make sure it matches this documentation.) If y already contains estimated dispersions, then no other arguments are required, and the existing dispersion values will be used. If y does not contain dispersions, then they will be estimated using design and .... Similarly, design is only required if y does not already contain a design (check if y$design is non-NULL).

DarwinAwardWinner/rctutils documentation built on July 22, 2022, 5:19 a.m.