Likelihood ratio test

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.

# S4 method for 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