07-Public-Dataset-Comparison.Rmd

---
title: "Public-Dataset-Comparison"
author: "Alexander Kirchmair"
params:
  data:    ../data/public
---

```{r setup, include=FALSE}
library(Seurat)
library(DESeq2)
library(limma)
library(datamisc)
library(dplyr)
```


Subset markers
```{r}
RNA <- list()
RNAmem <- readRDS(fp("../data", "RNAmem.rds"))
RNAexh <- readRDS(fp("../data", "RNAexh.rds"))

RNA$counts <- cjoin(RNAmem$counts, RNAexh$counts)
RNA$design <- full_join(mutate(RNAmem$design, Celltype = as.character(Celltype), Donor = as.character(Donor)),
                        mutate(RNAexh$design, Exp = NULL, Celltype = as.character(Celltype), Donor = as.character(as.numeric(Donor)+3)))
rownames(RNA$design) <- c(rownames(RNAmem$design), rownames(RNAexh$design))

RNA$markers <- getmarkers(as.matrix(RNA$counts)[,rownames(RNA$design)], RNA$design, group = "Celltype", formula = ~ group, log2FC > 1 & padj < 0.05)
RNA$markers <- lapply(RNA$markers, function(x){ x[1:min(length(x),200)] })
```


Comparison to public bulk RNA sequencing data
```{r}
public <- list()
public$bulk <- read.csv("../data/public/cd8_subset_profiles.csv", row.names = 1)
public$gsva_bulk <- runGSVA(public$bulk, genesets = RNA$markers)
colnames(public$gsva_bulk) <- paste0(colnames(public$gsva_bulk), " (public)")
```


Comparison to public single-cell RNA sequencing data
```{r}
if (!file.exists(fp(params$data, "CD8_Tcellmap.rds"))){
  download.file("https://singlecell.mdanderson.org/TCM/download/CD8",
                fp(params$data, "CD8_Tcellmap.rds"), method = "wget")
}
tcellmap <- readRDS(fp(params$data, "CD8_Tcellmap.rds"))

Idents(tcellmap) <- tcellmap$cell.type
tcellmap <- NormalizeData(tcellmap)
public$sc <- AverageExpression(tcellmap, group.by = "cell.type", assays = "RNA")[["RNA"]]
colnames(public$sc) <- make.names(colnames(public$sc))
public$sc <- public$sc[order(rowMeans(public$sc), decreasing = TRUE),]
public$gsva_sc <- runGSVA(public$sc[1:15000,], genesets = RNA$markers)

```


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