makeContrasts {limma} | R Documentation

## Construct Matrix of Custom Contrasts

### Description

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

### Usage

    makeContrasts(..., contrasts=NULL, levels)

### Arguments

`...` | expressions, or character strings which can be parsed to expressions, specifying contrasts
`contrasts` | character vector specifying contrasts
`levels` | character vector or factor giving the names of the parameters of which contrasts are desired, or a design matrix or other object with the parameter names as column names.

### Details

This function expresses contrasts between a set of parameters as a numeric matrix. The parameters are usually the coefficients from a linear model fit, so the matrix specifies which comparisons between the coefficients are to be extracted from the fit. The output from this function is usually used as input to `contrasts.fit`. The contrasts can be specified either as expressions using `...` or as a character vector through `contrasts`. (Trying to specify contrasts both ways will cause an error.)

The parameter names must be syntactically valid variable names in R and so, for example, must begin with a letter rather than a numeral. See `make.names` for a complete specification of what is a valid name.

### Value

Matrix which columns corresponding to contrasts.

### Author(s)

Gordon Smyth

### See Also

An overview of linear model functions in limma is given by 06.LinearModels.

### Examples

    makeContrasts(B-A,C-B,C-A,levels=c("A","B","C"))
    makeContrasts(contrasts="A-(B+C)/2",levels=c("A","B","C"))
    x <- c("B-A","C-B","C-A")
    makeContrasts(contrasts=x,levels=c("A","B","C"))

[Package limma version 2.8.1 Index]