Add PBMC Digestion Code

Author: samuel-marsh

10_PBMC Mock "Digestion" (Human)/01_Import & QC Filtering.R

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+# Environment Setup ---------------------------------------------------------------------------
+# R 3.6.1
+# Seurat 3.2.3
+# tidyverse 1.3.0
+# loomR 0.2.1.9000
+# Azimuth reference mapping was performed using online portal
+
+# Load Gene Lists for Module Scoring ----------------------------------
+# Gene lists available in SI Tables 04
+# Column 3 (Microglia Myeloid Shared Act Score)
+shared_sig <- "Load Microglia Meta Cell Score"
+shared_sig <- list(shared_sig)
+
+# Convert to human gene symbols (homologous gene names previously confirmed so just using simple gene name capitalization conversion)
+human_shared_sig <- lapply(shared_sig, function(x){str_to_upper(x)})
+
+# Setup project
+Setup_scRNAseq_Project()
+
+# Load Libraries & Data -----------------------------------------------------------------------
+library(tidyverse)
+library(Seurat)
+library(scCustomize)
+library(marsh.utils)
+library(patchwork)
+library(viridis)
+
+# Load Data 
+control <- Read10X(data.dir = ".../control/filtered_feature_bc_matrix/")
+
+inhib <- Read10X(data.dir = ".../inhib/filtered_feature_bc_matrix/")
+
+merged <- Merge_Sparse_Data_All(matrix_list = c(control, inhib), add_cell_ids = c("control", "inhib"))
+
+pbmc_mock_raw <- CreateSeuratObject(counts = merged, min.cells = 5, min.features = 200)
+
+# Add meta data
+pbmc_mock_raw <- Add_Mito_Ribo_Seurat(seurat_object = pbmc_mock_raw, species = "human")
+
+# QC Filter and Subset
+pbmc_mock_qc_filtered <- subset(x = pbmc_mock_raw, subset = nFeature_RNA > 400 & nFeature_RNA < 4500 & nCount_RNA < 22500 & percent_mito < 10)