| contrastMatrix {ArrayTools} | R Documentation |
Class to Contain the Contrast Matrix that Used for Linear Regression, inherited from the designMatrix class
new("contrastMatrix", ...,
design.matrix=[designMatrix],
compare1=[character],
compare2=[character],
level=[character],
interaction==[numeric]).
This creates a contrast matrix class. design.matrix is a designMatrix
class. compare1 the first value of the main covariate, and compare2
is the second value of the main covariate.
For example, suppose that the main covariate is "drug", and there
are three unique values: "drug1", "drug2", and "placebo".
You would like to compare "drug1" to "drug2". Then you would use "drug1" as
compare1 and "drug2" as compare2. If interaction==TRUE,
do not specify compare1 and compare2. You only specify
level when the design matrix contains an interaction term.
Suppose that you would like to compare "drug1" to "drug2" only when estrogen is
"present", where "present" is one of the values of the estrogen variable.
You will use "present" as level. If interaction==TRUE, do not specify this
value as well. You only specify interaction=TRUE when you would like to
detect the interaction effect between two covariates. In this case,
do not provide values for compare1, compare2, and level
contrast:"matrix" contains the contrast matrixcompare1:"character" contains compare1compare2:"character" contains compare2 level:"character" contains level interaction:"logical" contains interactiondesign:"matrix" contain the design matrixtarget:"data.frame" contains targetcovariates:"character" contains covariatesintIndex:"numeric" contains intIndex
Class "designMatrix", directly.
signature(object = "contrastMatrix"):
access the compare1 slotsignature(object = "contrastMatrix"):
access the compare2 slotsignature(object = "contrastMatrix"):
access the contrast slot signature(object = "contrastMatrix"):
access the interaction slotsignature(object = "contrastMatrix"):
access the level slot signature(.Object = "contrastMatrix"):
create a new contrast matrix class signature(object = "contrastMatrix"): print the contrast matrix Xiwei Wu, Arthur Li
data(eSetExample)
## One-way Anova
(design1<- new("designMatrix", target=pData(eSetExample), covariates = "Treatment"))
(contrast1<- new("contrastMatrix", design.matrix = design1,
compare1 = "Treated", compare2 = "Control"))
## Randomized block design
(design2<- new("designMatrix", target=pData(eSetExample),
covariates = c("Treatment", "Group")))
(contrast2<- new("contrastMatrix", design.matrix = design2,
compare1 = "Treated", compare2 = "Control"))
## Interaction design
(design3<- new("designMatrix", target=pData(eSetExample),
covariates = c("Treatment", "Group"), intIndex=c(1,2)))
# Test for interaction:
(contrast.int<- new("contrastMatrix", design.matrix = design3,
interaction=TRUE))
# Compare Treated vs Control among group A
(contrast.a<- new("contrastMatrix", design.matrix = design3,
compare1 = "Treated", compare2 = "Control", level="A"))