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Last data update: 2014.03.03

R: Reform a Design Matrix to that Contrasts Become Coefficients

contrastAsCoef

R Documentation

Reform a Design Matrix to that Contrasts Become Coefficients

Description

Reform a design matrix so that one or more coefficients from the new matrix correspond to specified contrasts of coefficients from the old matrix.

Usage

contrastAsCoef(design, contrast=NULL, first=TRUE)

Arguments

`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 (`TRUE`) or last columns (`FALSE`) of the output design matrix.

Details

If contrast doesn't have full column rank, then superfluous columns are dropped.

Value

A list with components

`design`	reformed design matrix
`coef`	columns of design matrix which hold the meaningful coefficients
`qr`	QR-decomposition of contrast matrix

Author(s)

Gordon Smyth

Examples

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(limma)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/limma/contrastAsCoef.Rd_%03d_medium.png", width=480, height=480)
> ### Name: contrastAsCoef
> ### Title: Reform a Design Matrix to that Contrasts Become Coefficients
> ### Aliases: contrastAsCoef
> ### Keywords: regression
> 
> ### ** Examples
> 
> 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)
   design1    design2    design3 
 0.3754279 -1.4508091 -0.1671291 
> coef(fit2)
 design2C1  design2Q2  design2Q3 
 1.2836800 -0.5435015 -1.0744367 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>