const-ae / const-ae/lemur

lemur::align_harmony causes an error with recent versions of harmony

Open
#29 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
R
Stars
102
Forks
11
PR merge metrics
No merged PRs in 30d

Description

Reproducible example: see https://github.com/Bioconductor/CSAMA-labs/tree/devel/multicond-scRNA-lemur code chunk "align-lemur-model".

```
fit2 <- lemur(sce, design = ~ stim, n_embedding = 30, verbose = FALSE)
fit2 <- align_harmony(fit2, verbose = FALSE)
```
**Error in `check_legacy_args()`:
! Argument max.iter is unhandled. Please refer to the documentation for the valid harmony options!**

Suggestions:

1.) preferentially: bug fix in the Bioconductor release of lemur, in time for CSAMA, second-best: a fix within the above lab qmd lab itself
2.) fix for next Bioconductor release, incl unit & integration test to pick up such problems automatically in the future

Thank you and kind regards
Wolfgang

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.