| 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 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.
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(fit1) coef(fit2)