contrasts {factDesign} | R Documentation |
'par2lambda' takes list of lm coefficient names and a corresponding list of numeric vectors corresponding to hypothesis tests of linear contrasts and returns a lambda matrix suitable for an F-test of the linear contrasts. 'par2lambda' is intended to be used in conjunction with 'contrastTest' or 'findFC'.
'contrastTest' performs an F test for simultaneous tests of linear contrasts using an appropriately specified lambda matrix and an lm object.
par2lambda(betaNames, betas, coefs) contrastTest(model, lambda, cVec = NA, p = 0.01)
betaNames |
A character vector of the names of the coefficients in a linear model. |
betas |
A list of vectors of the parameters to be used in the contrasts. |
coefs |
A list of vectors of numeric coefficients corresponding to betas. |
model |
An lm object. |
lambda |
A matrix of coefficients in the appropriate order to be multiplied by the estimated coefficients of the lm object, possibly returned from 'par2lambda'. |
cVec |
A vector of constants for testing that the linear contrasts equal something other than zero. If this is unspecified, it is assumed to be zero. |
p |
The significance level at which to perform the contrast test. |
For par2lambda
: A lambda matrix constructed for testing linear contrasts using lm output.
For contrastTest
:
test |
Returns "REJECT" or "FAIL TO REJECT" based on the result of the test of hypothesis. |
Fstat |
The F statistic for the test of contrast. |
pvalue |
The corresponding pvalue for the F test. |
cEst |
The contrast estimate. |
Denise Scholtens
data(estrogen) ES <- pData(estrogen)[["ES"]] TIME <- pData(estrogen)[["TIME"]] fit <- lm(exprs(estrogen)["40079_at",] ~ ES + TIME + ES*TIME) betaNames <- names(fit[["coef"]]) betas <- list(c("ESP"),c("ESP","ESP:TIME48h")) coefs <- list(c(1),c(1,1)) lambda <- par2lambda(betaNames,betas,coefs) contrastTest(fit,lambda)