contrastMatrix-class: Class to Contain the Contrast Matrix that Used for Linear...

In ArrayTools: geneChip Analysis Package

Description

Class to Contain the Contrast Matrix that Used for Linear Regression, inherited from the designMatrix class

Creating Objects

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

Slots

contrast:

Object of class "matrix" contains the contrast matrix

compare1:

Object of class "character" contains compare1

compare2:

Object of class "character" contains compare2

level:

Object of class "character" contains level

interaction:

Object of class "logical" contains interaction

design:

Object of class "matrix" contain the design matrix

target:

Object of class "data.frame" contains target

covariates:

Object of class "character" contains covariates

intIndex:

Object of class "numeric" contains intIndex

Extends

Class "designMatrix", directly.

Methods

getCompare1

signature(object = "contrastMatrix"): access the compare1 slot

getCompare2

signature(object = "contrastMatrix"): access the compare2 slot

getContrast

signature(object = "contrastMatrix"): access the contrast slot

getInteraction

signature(object = "contrastMatrix"): access the interaction slot

getLevel

signature(object = "contrastMatrix"): access the level slot

initialize

signature(.Object = "contrastMatrix"): create a new contrast matrix class

show

signature(object = "contrastMatrix"): print the contrast matrix

Author(s)

Xiwei Wu, Arthur Li

See Also

designMatrix

Examples

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"))

ArrayTools documentation built on Nov. 8, 2020, 8:13 p.m.