Error with DetectUTRLengthShift: GetAssayData() slot argument is defunct in SeuratObject 5.0.0+

[Shun-Yasui]

Error with DetectUTRLengthShift: GetAssayData() slot argument is defunct in SeuratObject 5.0.0+

Description

I'm encountering an error when running DetectUTRLengthShift() with the latest versions of Seurat and SeuratObject. The error indicates that the slot argument in GetAssayData() has been deprecated and is now defunct in SeuratObject 5.0.0+.

Error Message

Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.

Reproducible Example

library(Sierra)
library(Seurat)

# Running DetectUTRLengthShift
utr_shift_all <- DetectUTRLengthShift(
  peaks.object = PeakSeurat_996989_non_neuron,
  gtf_gr = gtf_gr,
  gtf_TxDb = gtf_TxDb,
  population.1 = population_NLGF_all,
  population.2 = population_WT_all
)

Environment

• Sierra version: 0.99.27
• Seurat version: 5.4.0
• SeuratObject version: 5.3.0
• R version: 4.2.0 (2022-04-22)

Expected Behavior

DetectUTRLengthShift() should run successfully and detect UTR length shifts between the two populations.

Actual Behavior

The function fails with an error about the defunct slot argument in GetAssayData().

Additional Context

This issue appears to be due to SeuratObject 5.0.0+ replacing the slot argument with layer in GetAssayData(). The Sierra package seems to still be using the old slot argument, which causes compatibility issues with newer versions of SeuratObject.

Temporary Workaround Attempted

I tried downgrading to SeuratObject 4.x, but this created additional compatibility issues with my Seurat objects that were created with version 5.x.

Suggested Fix

Update all instances of GetAssayData(..., slot = "...") to GetAssayData(..., layer = "...") throughout the Sierra package to ensure compatibility with SeuratObject 5.0.0+.

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