Prep_data_ex2.Rmd

---
title: "Exercise 1"
output: 
  html_document: 
    number_sections: true
    toc: true
---

This script was used to prepare the dataset for exercise 2

```{r, message=FALSE, warning=F, results=FALSE}

# Load the environment and libraries
renv::restore() # Run once, when you download a project folder and want to install all dependencies.
library(Seurat)
library(ggplot2)
library(dplyr)
```

# Load the data

```{r, message=FALSE, warning=F}
# Download data
download.file("https://www.dropbox.com/scl/fi/3ncxrapm374yk531m787f/Pre_P002_t.rds?rlkey=iv0afdro70cibv9wfa7ks67y4&dl=1",
              file.path(path_data, "Pre_P002_t.rds"))
download.file("https://www.dropbox.com/scl/fi/i6g6jt2u65q028r3ndph3/P14_Post-Tx.rds?rlkey=5uq1svqljct67w3lrocfgknk4&dl=1",
              file.path(path_data, "P14_Post-Tx.rds"))

obj.list <- list()
sample_study1 <- readRDS(file.path(path_data, "Pre_P002_t.rds"))
sample_study1 <- subset(sample_study1, downsample=500)
sample_study2 <- readRDS(file.path(path_data, "P14_Post-Tx.rds"))
sample_study2 <- subset(sample_study2, downsample=500)

obj.list[["study1_sample"]] <- sample_study1
obj.list[["study1_sample"]]$orig.ident <- "study1_sample"
obj.list[["study2_sample"]] <- sample_study2
obj.list[["study2_sample"]]$orig.ident <- "study2_sample"
obj.list[["study2_sample"]]@meta.data[["scGate_multi"]][which(obj.list[["study2_sample"]]@meta.data[["scGate_multi"]] == "CD8TIL")] <- "CD8T"
obj.list[["study2_sample"]]@meta.data[["scGate_multi"]][which(obj.list[["study2_sample"]]@meta.data[["scGate_multi"]] == "Bcell.NonGerminalCenter")] <- "Bcell"

saveRDS(obj.list, file=file.path(path_data, "samples_from_other_studies.rds"))
```