contrastAsCoef: Reform a Design Matrix to that Contrasts Become Coefficients
In richierocks/limma2: Linear Models for Microarray Data

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`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.

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

A list with components

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

Gordon Smyth

model.matrix in the stats package.

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

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)