week3_final_code.Rmd

---
title: "Week 3 Final Code"
---

For completeness, here is the code to read the salmon counts and convert to a DESeq2 dataset.

```{r}
library(readr)
library(tximport)
dirs <- list.files("salmon_quant/")
quant_files <- list.files("salmon_quant/",pattern="quant.sf.gz",recursive = TRUE,full.names = TRUE)
names(quant_files) <- dirs
```


```{r}
tx2gene <- read_csv("tx2gene.csv")
txi <- tximport(quant_files,
                type="salmon",
                tx2gene = tx2gene,
                ignoreTxVersion = TRUE)
```


```{r}
sampleinfo <- read_csv("meta_data/sampleInfo.csv")
library(DESeq2)
dds <- DESeqDataSetFromTximport(txi, 
                                colData = sampleinfo,
                                design = ~Treated)
```


```{r}
library(dplyr)
library(ggplot2)
## if we want the same colour for each bar we can change the fill argument in geom_col

mutate(sampleinfo, LibSize  = colSums(counts(dds)) / 1e6) %>% 
  ggplot(aes(x = LibSize, y = Run)) + geom_col(fill="steelblue") + geom_vline(xintercept = 20,col="red")
```