05-RNA-Exhaustion-Public.Rmd

---
title: "05-RNA-Exhaustion-Public"
author: "Alexander Kirchmair"
params:
  data:    ../data/public
---

```{r setup, include=FALSE}
library(GEOquery)
library(DESeq2)
library(datamisc)

dir.create(params$data, showWarnings = FALSE)
```


## Download data
```{r}
geo <- getGEO("GSE210534", GSEMatrix = FALSE, destdir = params$data)
geosupp <- getGEOSuppFiles("GSE210534", baseDir = params$data)
gunzip(rownames(geosupp))

```


## Differential expression analysis
```{r}
data <- readRDS(fp(params$data, "GSE210534/GSE210534_ensdb_105_dge_list_final.rds"))
data$gene_counts <- collapse(data$counts[data$genes$SYMBOL != "",], ids = data$genes$SYMBOL[data$genes$SYMBOL != ""], average_by = sum)

data$contrasts <- list(TeffvsTrest = c("SampleGroup", "Teff", "Trest"),
                       TexvsTrest = c("SampleGroup", "Tex", "Trest"),
                       TtumorvsTrest = c("SampleGroup", "Ttumor", "Trest"),
                       TexvsTtumor = c("SampleGroup", "Tex", "Ttumor"),
                       TexvsTeff = c("SampleGroup", "Tex", "Teff"))

data$DE <- runDESeq2(as.matrix(round(data$gene_counts)),
                     ncores = 1,
                     design = data$samples,
                     formula = ~ SampleGroup + Donor,
                     contrasts = data$contrasts)

```


```{r}
saveRDS(data, "../data/GSE210534_data.rds")
```