makeContrasts: Construct Matrix of Custom Contrasts In limma: Linear Models for Microarray Data

Description

Construct the contrast matrix corresponding to specified contrasts of a set of parameters.

Usage

 `1` ```makeContrasts(..., contrasts=NULL, levels) ```

Arguments

 `...` expressions, or character strings which can be parsed to expressions, specifying contrasts `contrasts` character vector specifying contrasts `levels` character vector or factor giving the names of the parameters of which contrasts are desired, or a design matrix or other object with the parameter names as column names.

Details

This function expresses contrasts between a set of parameters as a numeric matrix. The parameters are usually the coefficients from a linear model fit, so the matrix specifies which comparisons between the coefficients are to be extracted from the fit. The output from this function is usually used as input to `contrasts.fit`. The contrasts can be specified either as expressions using `...` or as a character vector through `contrasts`. (Trying to specify contrasts both ways will cause an error.)

The parameter names must be syntactically valid variable names in R and so, for example, must begin with a letter rather than a numeral. See `make.names` for a complete specification of what is a valid name.

Value

Matrix which columns corresponding to contrasts.

Author(s)

Gordon Smyth

An overview of linear model functions in limma is given by the help page 06.LinearModels.

Examples

 ```1 2 3 4``` ```makeContrasts(B-A,C-B,C-A,levels=c("A","B","C")) makeContrasts(contrasts="A-(B+C)/2",levels=c("A","B","C")) x <- c("B-A","C-B","C-A") makeContrasts(contrasts=x,levels=c("A","B","C")) ```

Example output

```      Contrasts
Levels B - A C - B C - A
A    -1     0    -1
B     1    -1     0
C     0     1     1
Contrasts
Levels A-(B+C)/2
A       1.0
B      -0.5
C      -0.5
Contrasts
Levels B-A C-B C-A
A  -1   0  -1
B   1  -1   0
C   0   1   1
```

limma documentation built on Nov. 8, 2020, 8:28 p.m.