nullMatrix: Matrix representation of null model

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

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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

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# 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 May 6, 2019, 4:58 a.m.