NEWS.md

In kieranrcampbell/clonealign: Assigning scRNA-seq to clone-of-origin using copy number from ultra-low-depth scDNA-seq

clonealign 2.0

Clonealign 2.0 contains several updated changes, both to the core model and inference, as well as to package functionality.

Major changes:

• While the modelled expectation remains identical, the likelihood employed is now multinomial rather than negative binomial. This speeds up inference and removes the need for size factor and variance calculation.
• The preferred package entrypoint is the run_clonealign function, that will run clonealign across a range of initial parameter values and return the fit that maximizes the ELBO.

New functionality

• Post-hoc calculated correlations between the copy number and gene expression are calculated and assigned to the $correlations slot

Changes to the core model

• Multinomial likelihood rather than negative binomial
• mu[1] no longer constrained to be 1 to improve optimization in some cases
• It is no longer necessary to specify size factors as the multinomial distribution implicitly conditions on the total counts per cell

Changes to inference

• Convergence is monitored by looking at the average change in the previous 10 iterations rather than the single previous iteration, which can be sensitive to random fluctuations

kieranrcampbell/clonealign documentation built on Dec. 18, 2020, 3:49 a.m.