Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/contrastAsCoef.R

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

1 | ```
contrastAsCoef(design, contrast=NULL, first=TRUE)
``` |

`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 ( |

If the contrasts contained in the columns of `contrast`

are not linearly dependent, then superfluous columns are dropped until the remaining matrix has full column rank.
The number of retained contrasts is stored in `qr$rank`

and the retained columns are given by `qr$pivot`

.

A list with components

`design` |
reformed design matrix |

`coef` |
columns of design matrix which hold the meaningful coefficients |

`qr` |
QR-decomposition of contrast matrix |

Gordon Smyth

`model.matrix`

in the stats package.

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

1 2 3 4 5 6 7 8 9 10 11 |

```
design1 design2 design3
-0.1032381 0.2882667 0.9806105
design1 design2 design3
-0.1032381 0.2882667 0.9806105
design2C1 design2Q2 design2Q3
0.6923438 0.5614383 0.7074390
```

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