size_factors parameter

[gianasco]

Hi @kieranrcampbell, Congratulations for this amazing tool! I have one equation about one parameter I cannot find how to set. The help function for "clonealign::clonealign" discusses a "size_factors" parameter that can be set to "infer" or "fixed", which if I well understand is "s_n" of the main clonealign equation (correct?). However, the actual function definition does not have such parameter. Has the option been taken off or maybe set by "infer" as default?

[kieranrcampbell]

Hi @gianasco

At some point last year the model for clonealign changed from using a negative binomial likelihood to multinomial, for speed amongst other things. As a consequence of that, the "size factors" are now just the total reads per cell for each cell. So in a way they are "infer" by default -- I will update the documentation to reflect this.

Kieran