search

ebi-gene-expression-group / monocle-scripts

Command line scripts wrapping functions in monocle3
8 stars 1 forks source link

Add option for sparse matrix parsing when creating CDS #5

Closed a-solovyev12 closed 4 years ago

a-solovyev12 commented 4 years ago

This PR adds ability to read sparse matrices in .mtx format when creating CDS object.

nh3 commented 4 years ago

Very good addition! Perhaps also mention this in the usage message? https://github.com/ebi-gene-expression-group/monocle-scripts/blob/b39b0f22fa3701ce31f7259ecf109de414ed3a90/R/cmd_args.R#L124

nh3 commented 4 years ago

Would be great if the tests can be updated to use mtx input, since I imagine it will be the main input format when put to use.

a-solovyev12 commented 4 years ago

@nh3 Updating the tests is definitely a good idea. Do you know if there is a link to the same dataset in .mtx format somewhere? Otherwise, I can write a function to extract the matrix from .rds object and stick it into downstream test cases.

nh3 commented 4 years ago

I am not aware of an mtx version of the same dataset online. I think your solution is very reasonable.

a-solovyev12 commented 4 years ago

Thank you for review @nh3

a-solovyev12 commented 4 years ago

Hi @nh3, could you please make a release with updated version? I'd like to incorporate this into a workflow I'm working on. Thanks!

nh3 commented 4 years ago

Hi @a-solovyev12, I've given you permissions to release it on your own.