Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix/run slsi.std assay no npcs binding #9545

Merged
merged 2 commits into from
Dec 17, 2024

Conversation

dcollins15
Copy link
Contributor

Drops reference to npcs variable from RunSLSI.StdAssay. Since npcs is not defined, the following NOTE to be thrown during CRAN checks:

❯ checking R code for possible problems ... [40s/40s] NOTE
  RunSLSI.StdAssay: no visible binding for global variable ‘npcs’
  Undefined global functions or variables:
    npcs

In lieu of any tests, the following script can be used to quickly verify RunSLSI is still working as expected:

library(Seurat)
library(Signac)
library(BPCells)

# Convert "peaks" to an `Assay5` instance.
atac_small[["peaks"]] <- as(atac_small[["peaks"]], Class = "Assay5")
# `RunSLSI` should not raise any errors when passed a `StdAssay`.
atac_small <- RunSLSI(
  atac_small,
  graph = "peaks_snn",
  assay = "peaks"
)

# The same should be true for an `Assay5` instance holding a
# `BPCells::IterableMatrix`.
atac_small[["peaks"]]$data <- as(
  atac_small[["peaks"]]$data,
  Class = "IterableMatrix"
)
atac_small <- RunSLSI(
  atac_small,
  graph = "peaks_snn",
  assay = "peaks"
)

Relates to:

@dcollins15 dcollins15 force-pushed the fix/RunSLSI.StdAssay-no-npcs-binding branch from c640105 to 8941be9 Compare December 17, 2024 12:44
@dcollins15 dcollins15 marked this pull request as ready for review December 17, 2024 12:56
@dcollins15 dcollins15 merged commit d015357 into develop Dec 17, 2024
3 checks passed
@dcollins15 dcollins15 deleted the fix/RunSLSI.StdAssay-no-npcs-binding branch December 17, 2024 21:38
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants