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quadbio / Pando

Multiome GRN inference.
https://quadbio.github.io/Pando/
MIT License
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issue in initiate_grn- invalid class "Seurat" object: 'assays' must be a named list #54

Closed heteyszabolcs closed 4 months ago

heteyszabolcs commented 5 months ago

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

Qotov commented 5 months ago

https://github.com/quadbio/Pando/issues/40

heteyszabolcs commented 5 months ago

These versions solved my problem: _Signac_1.11.0, SeuratObject_4.1.4 , Seurat4.3.0 Thanks!

joschif commented 4 months ago

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.

joschif commented 4 months ago

Closing this for now, feel free to reopen if issues persist