contrastAsCoef {limma} | R Documentation

## Reform a Design Matrix to that Contrasts Become Coefficients

### Description

Reform a design matrix so that one or more coefficients from the new matrix correspond to specified contrasts of coefficients from the old matrix.

### Usage

    contrastAsCoef(design, contrast=NULL, first=TRUE)

### Arguments

`design` | numeric design matrix.
`contrast` | numeric matrix with rows corresponding to columns of the design matrix (coefficients) and columns containing contrasts. May be a vector if there is only one contrast.
`first` | logical, should coefficients corresponding to contrasts be the first columns (`TRUE`) or last columns (`FALSE`) of the output design matrix.

### Details

If the contrasts contained in the columns of `contrast` are not linearly dependent, then superfluous columns are dropped until the remaining matrix has full column rank. The number of retained contrasts is stored in `qr$rank` and the retained columns are given by `qr$pivot`.

### Value

A list with components

`design` | reformed design matrix
`coef` | columns of design matrix which hold the meaningful coefficients
`qr` | QR-decomposition of contrast matrix

### Author(s)

Gordon Smyth

### See Also

`model.matrix` in the stats package.

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

### Examples

    design <- cbind(1,c(0,0,1,1,0,0),c(0,0,0,0,1,1))
    cont <- c(0,-1,1)
    design2 <- contrastAsCoef(design, cont)$design

    #  Original coef[3]-coef[2] becomes coef[1]
    y <- rnorm(6)
    fit1 <- lm(y~0+design)
    fit2 <- lm(y~0+design2)
    coef(fit1)
    coef(fit1)
    coef(fit2)

[Package limma version 3.42.2 Index]