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kieranrcampbell / clonealign

Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data
Apache License 2.0
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size_factors parameter #13

Open gianasco opened 4 years ago

gianasco commented 4 years ago

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 commented 4 years ago

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