issue in initiate_grn- invalid class "Seurat" object: 'assays' must be a named list
heteyszabolcs opened this issue · comments
object <- as(object, 'SeuratPlus') line of the "initiate_grn" function doesn't return SeuratPlus object and crashes the grn initiation. My code is here:
init_grn = initiate_grn(
coembed,
rna_assay = "RNA",
peak_assay = "peaks",
exclude_exons = FALSE,
regions = regions
)
My input object looks like this:
An object of class Seurat
367556 features across 16674 samples within 3 assays
Active assay: peaks (326427 features, 326427 variable features)
2 layers present: counts, data
2 other assays present: RNA, GA
2 dimensional reductions calculated: pca, umap
my assays:
coembed@assays
_$RNA
Assay (v5) data with 21522 features for 16674 cells
Top 10 variable features:
PMP22, DLK1, COL3A1, NPPB, PGF, ACTC1, LUM, FN1, KRT18, HAND1
Layers:
counts.scRNA_EZH2i, data.scRNA_EZH2i, scale.data.scRNA_EZH2i, data.SeuratProject, scale.data
$peaks
ChromatinAssay data with 326427 features for 12612 cells
Variable features: 326427
Genome:
Annotation present: TRUE
Motifs present: FALSE
Fragment files: 1
$GA
Assay data with 19607 features for 12612 cells
First 10 features:
PLCXD1, GTPBP6, PPP2R3B, SHOX, CRLF2, CSF2RA, IL3RA, SLC25A6, ASMTL, P2RY8_
Error message:
Error in validObject(object = .Object) :
invalid class "Seurat" object: 'assays' must be a named list
My session:
other attached packages:
[1] Pando_1.0.5 EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.26.0 AnnotationFilter_1.26.0 ggpubr_0.6.0 GenomicFeatures_1.52.2 AnnotationDbi_1.64.1 Biobase_2.62.0
[9] rtracklayer_1.62.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.5 IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1 lubridate_1.9.3 forcats_1.0.0
[17] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.4 tidyverse_2.0.0
[25] glue_1.6.2 Signac_1.12.0 Seurat_5.0.1 SeuratObject_5.0.1 sp_2.1-2
These versions solved my problem: Signac_1.11.0, SeuratObject_4.1.4 , Seurat_4.3.0
Thanks!
Hi everyone, I finally got around to updating Pando to be compatible with Seurat v5, which I believe should fix these issues. The new Pando version v1.1.0 is now incompatible with previous Seurat versions though.
Closing this for now, feel free to reopen if issues persist