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Applies shrinkage to the regression coefficients in the discrete (logistic) part of the hurdle model. Default is Enabled. The initial versions of MAST contained a bug that was fixed in its R source in March 2020. However, for the sake of reproducibility the fix was released only on a topic branch in MAST Github [2] and the default version of MAST remained as is. To install the fixed version of MAST in R, run the following R script.

# Uninstall the default version of MAST, if it's installed.
remove.packages("MAST")
# Install devtools, if it's not installed yet.
library("devtools")
install_github("https://github.com/RGLab/MAST/tree/fix/bayesglm")
library(MAST)

In Flow, the user can switch between the fixed and default version by selecting Fixed version or Default version, respectively. To disable the shrinkage altogether, choose Disabled.

References

[1] Finak, G., McDavid, A., Yajima, M., Deng, J., Gersuk, V., Shalek, A. K., ... & Linsley, P. S. (2015). MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome biology, 16(1), 278.

[2] MAST topic branch that contains the regression coefficient shrinkage fix:

https://github.com/RGLab/MAST/tree/fix/bayesglm

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