nullModel: Null model equation from deSet object

In edge: Extraction of Differential Gene Expression

Description

These generic functions access and set the null model for deSet object.

Usage

nullModel(object)

nullModel(object) <- value

## S4 method for signature 'deSet'
nullModel(object)

## S4 replacement method for signature 'deSet'
nullModel(object) <- value

Arguments

object	S4 object: deSet
value	formula: The experiment design for the null model.

Value

nullModel returns the formula for the null model.

Author(s)

John Storey, Andrew Bass

See Also

deSet

Examples

# import data
library(splines)
data(kidney)
age <- kidney$age
sex <- kidney$sex
kidexpr <- kidney$kidexpr
cov <- data.frame(sex = sex, age = age)

# create models
null_model <- ~sex
full_model <- ~sex + ns(age, df = 4)

# create deSet object from data
de_obj <- build_models(data = kidexpr, cov = cov, null.model = null_model,
full.model = full_model)

# extract the null model equation
mod_null <- nullModel(de_obj)

# change null model in experiment but must update full model
nullModel(de_obj) <- ~1
fullModel(de_obj) <- ~1 + ns(age, df=4)

edge documentation built on Nov. 8, 2020, 6:48 p.m.