[Bioc-devel] Splitting design matrix contrast pivoting logic into a separate function?

Gordon K Smyth smyth at wehi.EDU.AU
Mon Sep 2 00:15:06 CEST 2013

Dear Ryan,

See contrastAsCoef() in limma 3.17.23.

Best wishes

Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.

On Thu, 29 Aug 2013, Ryan C. Thompson wrote:

> Hi Gordon,
> I am currently working on some code that would benefit from having direct 
> access to the code in edgeR::glmLRT that handles reparametrizing the design 
> matrix so that the N linearly independent components of the specified 
> contrasts are represented in the first N columns of the design matrix (i.e. 
> the part of glmLRT that does all the QR decomposition stuff). Would you 
> consider splitting this logic into a separate function that takes a design 
> matrix and contrast matrix and returns the equivalent reparametrized design 
> matrix and vector of coefficients?
> Thanks,
> -Ryan Thompson

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