| contrastAsCoef {limma} | R Documentation |
Reform a design matrix so that one or more coefficients from the new matrix correspond to specified contrasts of coefficients from the old matrix.
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 ( |
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)