---
title: "12-DEG-enrich"
author: "Steven Roberts"
date: "`r format(Sys.time(), '%d %B, %Y')`"  
output: 
  github_document:
    toc: true
    toc_depth: 3
    number_sections: true
    html_preview: true
  html_document:
    theme: readable
    highlight: zenburn
    toc: true
    toc_float: true
    number_sections: true
    code_folding: show
    code_download: true
editor_options: 
  markdown: 
    wrap: sentence
---

```{r setup, include=FALSE}
library(knitr)
library(tidyverse)
library(kableExtra)
library(DT)
library(Biostrings)
library(tm)
library(pheatmap)
library(DESeq2)
knitr::opts_chunk$set(
  echo = TRUE,         # Display code chunks
  eval = FALSE,         # Evaluate code chunks
  warning = FALSE,     # Hide warnings
  message = FALSE,     # Hide messages
  fig.width = 6,       # Set plot width in inches
  fig.height = 4,      # Set plot height in inches
  fig.align = "center", # Align plots to the center
  comment = ""         # Prevents appending '##' to beginning of lines in code output
)
```


DEG list

```{r, eval=TRUE}
deglist <- read.csv("../output/10-hisat-deseq2/DEGlist.tab", sep = '\t', header = TRUE)
deglist$RowName <- rownames(deglist)
deglist2 <- deglist[, c("RowName", "pvalue")] # Optionally, reorder the columns
```

```{r, eval=TRUE}
head(deglist)
```

```{r, evalue=TRUE}
deglistID <- deglist %>% mutate(geneID = sub(".*\\|", "", RowName))
```

```{r, evalue=TRUE}
head(deglistID)
```
5061 DEGs


Annotation of Cod

```{r, eval=TRUE}
blast <- read.csv("../output/11-annotation/PcodRNA_uniprot_blastx.tab", sep = '\t', header = FALSE)
```


```{r, eval=TRUE}
head(blast)
```

```{r, eval=true}
rnatabID <- read.csv("../output/11-annotation/rnatabID.tab", sep = '\t', header = TRUE)
```


```{r, evalue=true}
head(rnatabID)
```

Count matrix


```{r, eval=true}
gcm <- read.csv("../output/10-hisat-deseq2/gene_count_matrix.csv", sep = ',', header = TRUE)
```

```{r, eval=true}
head(gcm)
```

Join DEGList with cod annotation

```{r, eval=TRUE}
degannot <-
  left_join(deglistID, rnatabID,  by = "geneID") %>%
  select(geneID, V1, V2, padj) %>%
  left_join(blast, by = "V1")

```