adding annoFuse for kinase status

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

Adding annoFuse to docker to get pfam domain annotation and kinase domain status

What was your approach?

Added
RUN R -e "BiocManager::install(c('EnsDb.Hsapiens.v86', 'ensembldb'))"
RUN R -e "remotes::install_github('d3b-center/annoFuse', dependencies = TRUE)"

What GitHub issue does your pull request address?

#812

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Adding annoFuse will make adding kinase domain status 1 line command by running something similar to the example in the function here:
https://github.com/d3b-center/annoFuse/blob/master/R/fusion_driver.R

So do we want to use this function from annoFuse or replicate the internal functions fusion_driver() and get_Pfam_domain() in OpenPBTA?
Asking mainly for

• some aggregating steps will need to be updated to keep LeftBreakpoint and RightBreakpoint columns so domain retention status can be added with respect to where the breakpoints are within the genes
• consistency, since the other scripts in fusion_filtering are base functions and not functions called from annoFuse?

Is there anything that you want to discuss further?

NA

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

No

Results

What types of results are included (e.g., table, figure)?

NA

What is your summary of the results?

NA

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[jharenza]

So do we want to use this function from annoFuse or replicate the internal functions fusion_driver() and get_Pfam_domain() in OpenPBTA?

I think we can use from annoFuse directly.

[jashapiro]

Please follow the instructions in https://github.com/AlexsLemonade/OpenPBTA-analysis#docker-image for adding packages to the docker image. In particular, note that BiocManager::install() should not be used. Please use install_bioc.R instead. Also, any packages installed from github must include a specific commit id.

If annoFuse requires a more recent version of tidyverse than we currently have in the image, this will require special accommodations in order to not break other modules.

[kgaonkar6]

Thanks for the link @jashapiro

Yeah it seems annoFuse imports tidyr::one_of() which was only added to tidyr1.02 or later but we have tidyr0.8.3 in openpbat docker so I was trying to update the version but without luck.

Do you think we can update the tidyr to 1.0.2 or I was gonna try changing the @importFrom to dplyr::one_of() in a branch of annoFuse to check if that works in the docker.

[jashapiro]

Yeah it seems annoFuse imports tidyr::one_of() which was only added to tidyr1.02 or later but we have tidyr0.8.3 in openpbat docker so I was trying to update the version but without luck.

Do you think we can update the tidyr to 1.0.2 or I was gonna try changing the @importFrom to dplyr::one_of() in a branch of annoFuse to check if that works in the docker.

Unfortunately, updating tidyr is a pretty big project given the other dependencies across the project and the major changes that came with 1.0. We might be able to come up with a solution, but it may not be straightforward. If you do need one_of then using the dplyr version is probably the best solution for now, and that can be installed pretty easily by pointing install_github() to a commit on that branch.

[kgaonkar6]

Importing one_of from dplyr seems to have worked! Thanks!

[jashapiro]

Looks good! Looking forward to seeing the analysis this enables!