Outdated vignette and lack of documentation

[SergejRuff]

Hello,

I am trying to understand MuSiC and MuSiC2. So I started reading the Vignette uploaded to https://xuranw.github.io/MuSiC/articles/MuSiC.html . Sadly, the vignette seems to be outdated, as (for example) some arguments in the vignette are no longer named the same in the function, leading to an error, when running the code in the vignette.

The documentation in the R package itself is also lackluster. It would be great, if an updated version of the package could provide an internal example dataset, examples in the documentation (after @examples section), and a details section explaining what the function does and how it is implemented.

For instance, music_prop() generates two matrices as output

Est.prop.weighted
Est.prop.allgene

What both of these matrices represent is unclear and the vignette uses both but offers no interpretation of both. Could you explain what both matrices are and update the documentation of the vignette and the R package itself