makeContrast {msqrob2} | R Documentation

## Make contrast matrix

### Description

Construct the contrast matrix corresponding to specified contrasts of a set of parameters.

### Usage

    makeContrast(contrasts, parameterNames)

### Arguments

`contrasts` | character vector specifying contrasts, i.e. the linear combination of the modelparameters that equals to zero.
`parameterNames` | character vector specifying the model parameters that are involved in the contrasts, e.g if we model data of three conditions using a factor condition with three levels a, b and c then our model will have 3 mean parameters named (Intercept), conditionb and conditionc. Hence the log2 fold change between b and a is conditionb. Under the null hypothesis the log2 fold change equals 0. Which is to be encoded as "conditionb=0". If we would like to test for log2 fold change between condition c and b we assess if the log2 fold change conditionc-conditionb equals 0, encoded as "condtionb-conditionc=0".

### Value

A numeric contrast matrix with rownames that equal the model parameters that are involved in the contrasts

### Examples

    makeContrast(c("conditionb = 0"),
        parameterNames = c(
            "(Intercept)",
            "conditionb",
            "conditionc"
        )
    )
    makeContrast(c("conditionc=0"),
        parameterNames = c("conditionc")
    )
    makeContrast(c(
        "conditionb=0",
        "conditionc=0",
        "conditionc-conditionb=0"
    ),
    parameterNames = c(
        "conditionb",
        "conditionc"
    )
    )

[Package msqrob2 version 1.0.0 Index]