# Load relevant libraries
library(Seurat)
library(SeuratDisk)
library(tidyverse)

# Download DropletUtils
#BiocManager::install("DropletUtils")
library(DropletUtils)

# Let's call out the vtdataset
vtdataset <-  readRDS("/home/youkim/MetaMarkers/4-dataset-test/vtSeurat2_annotated.rds")
sdataset <-  readRDS("/home/youkim/MetaMarkers/4-dataset-test/sSeurat_20230515.rds")
ldataset <- readRDS("/home/youkim/MetaMarkers/4-dataset-test/lSeurat_annotated.rds")
hdataset <- readRDS("/home/youkim/MetaMarkers/4-dataset-test/hSeurat_annotated.rds")
adataset <- readRDS("/home/youkim/Meta-analysis/Arutyanyan_et_al.2023/aSeurat_analyzed.rds")
cdataset <- readRDS("/home/youkim/Meta-analysis/Term_Placenta/Campbell_et_al.2023/cSeurat_20230521.rds")

# Extract the count matrix
count_matrix <- Seurat::GetAssayData(vtdataset, assay = "RNA")
count_matrix_s <- Seurat::GetAssayData(sdataset, assay = "RNA")
count_matrix_l <- Seurat::GetAssayData(ldataset, assay = "RNA")
count_matrix_h <- Seurat::GetAssayData(hdataset, assay = "RNA")
count_matrix_a <- Seurat::GetAssayData(adataset, assay = "RNA")
count_matrix_c <- Seurat::GetAssayData(cdataset, assay = "RNA")

# Interestingly, the following code will run into an error.
# This is because the count matrices that we're operating on are already filtered!
# EDcheck <- emptyDrops(count_matrix)
# EDcheck <- emptyDrops(count_matrix_s)
# EDcheck <- emptyDrops(count_matrix_l)
# EDcheck <- emptyDrops(count_matrix_h)
# EDcheck <- emptyDrops(count_matrix_a)
# EDcheck <- emptyDrops(count_matrix_c)