nullMatrix: Matrix representation of null model

In edge: Extraction of Differential Gene Expression

Description

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

Usage

nullMatrix(object)

nullMatrix(object) <- value

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

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

Arguments

object	S4 object: deSet
value	matrix: null model matrix where columns are covariates and rows are observations

Value

nullMatrix returns the value of the null model matrix.

Author(s)

John Storey, Andrew Bass

See Also

deSet, fullModel and fullModel

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 as a matrix
mat_null <- nullMatrix(de_obj)

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