lrTest-ZlmFit-character-method: Likelihood ratio test

In RGLab/MAST: Model-based Analysis of Single Cell Transcriptomics

Likelihood ratio test

Description

A 3D array with first dimension being the genes, next dimension giving information about the test (the degrees of freedom, Chisq statistic, and P value), and final dimension being the value of these quantities on the discrete, continuous and hurdle (combined) levels.

Usage

## S4 method for signature 'ZlmFit,character'
lrTest(object, hypothesis, ...)

Arguments

object	ZlmFit
hypothesis	See Details
...	Arguments passed on to zlm formula a formula with the measurement variable on the LHS and predictors present in colData on the RHS sca SingleCellAssay object method character vector, either 'glm', 'glmer' or 'bayesglm' silent Silence common problems with fitting some genes ebayes if TRUE, regularize variance using empirical bayes method ebayesControl list with parameters for empirical bayes procedure. See ebayes. force Should we continue testing genes even after many errors have occurred? hook a function called on the fit after each gene. parallel If TRUE and option(mc.cores)>1 then multiple cores will be used in fitting. LMlike if provided, then the model defined in this object will be used, rather than following the formulas. This is intended for internal use. onlyCoef If TRUE then only an array of model coefficients will be returned (probably only useful for bootstrapping). exprs_values character or integer passed to 'assay' specifying which assay to use for testing

Value

3D array

RGLab/MAST documentation built on Sept. 30, 2023, 1:08 p.m.