dyno_TI_Method_selection

Load Libraries

Loading required namespace: SeuratObject

library(dyno)
library(tidyverse)

Load Main Seurat Object

# Load your main Seurat object containing all samples, already SCTransformed
dataset <- readRDS("../0-Seurat_RDS_OBJECT_FINAL/Seurat_object_Final_changes/All_samples_Merged_with_STCAT_Annotation_final-5-09-2025.rds")
gc()

             used   (Mb) gc trigger    (Mb)   max used   (Mb)
Ncells     970371   51.9    1776707    94.9    1347338   72.0
Vcells 1219155040 9301.5 1510826741 11526.7 1219159181 9301.5

library(Seurat)

counts <- as.matrix(GetAssayData(dataset, slot = "counts"))

expression <- as.matrix(GetAssayData(dataset, slot = "data"))


dyno_dataset <- wrap_expression(
  counts = counts,
  expression = expression
)

gc()

             used    (Mb) gc trigger    (Mb)   max used    (Mb)
Ncells    4013131   214.4    8047345   429.8    4747395   253.6
Vcells 4318469835 32947.4 5482753630 41830.1 4319953358 32958.7

methods_selected

[1] "paga"