bugfix RcppML::nmf + fgsea error message #1
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Hey guys,
regarding this issue:
dibbelab#6 (comment)
I fixed the RcppML::nmf function so that the keyword argument is not refuted by Rcpp. (Lines 194, 208, 215)
Further, RcppML::nmf returns a list, which is why I changed the code to $ accession compared to @. (following the RcppML::nmf function call)
Running runScGSEA with this prompted an error with a custom pathway list where fgsea said "stats should be named" (https://rdrr.io/bioc/fgsea/src/R/fgsea.R), which could be resolved by adding rownames that I took from the rawCounts slot.
I tested the changes with a custom set of genes in my custom dataset as well as with the hallmarks on my custom dataset, both worked fine.
Thank you very much for the package!