limma (version 3.28.14)

contrastAsCoef: 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.

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

Details

If contrast doesn't have full column rank, then superfluous columns are dropped.

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(fit2)