getContrast,StatModel-method {msqrob2}

R Documentation

Methods for StatModel class

Description

Methods for StatModel class

getContrast(object, L)

to calculate contrasts of the model parameters

varContrast(object, L)

to calculate the variance-covariance matrix of the contrasts

Usage

## S4 method for signature 'StatModel'
getContrast(object, L)

## S4 method for signature 'StatModel'
varContrast(object, L)

Arguments

object	A list with elements of the class StatModel that are estimated using the msqrob function
L	contrast numeric matrix specifying one or more contrasts of the linear model coefficients to be tested equal to zero. The rownames of the matrix should be equal to the names of parameters of the model.

Value

A matrix with the calculated contrasts or variance-covariance matrix of contrasts

Examples

data(pe)
# Aggregate peptide intensities in protein expression values
pe <- aggregateFeatures(pe, i = "peptide", fcol = "Proteins", name = "protein")

# Fit msqrob model
pe <- msqrob(pe, i = "protein", formula = ~condition)

# Define contrast
getCoef(rowData(pe[["protein"]])$msqrobModels[[1]])
# Define contrast for log2 fold change between condition c and condition b:
L <- makeContrast("conditionc - conditionb=0", c("conditionb", "conditionc"))

getContrast(rowData(pe[["protein"]])$msqrobModels[[1]], L)
varContrast(rowData(pe[["protein"]])$msqrobModels[[1]], L)

---