05-merge-blast-to-DEG-list

Author

Sarah Tanja

Published

May 18, 2023

Install Packages

if ("tidyverse" %in% rownames(installed.packages()) == 'FALSE') install.packages('tidyverse')
if ("ggplot2" %in% rownames(installed.packages()) == 'FALSE') install.packages('ggplot2')

Load Libraries

library(tidyverse)
library(ggplot2)

Merge the annotated table with the DEGlist

If you take a look at the DEGlist.tab, you will see that the row names themselves are the gene ID’s. This contrasts with the blast GO anotated table that has a whole column (V1) dedicated to the gene ID in the same format. Thus, we first need to take the row names of the DEGlist.tab and make them into a new column. It was originally in it’s own column but we needed to convert it so that it could go through the DESeq workflow.

bash

cd ../output/deseq
head -n 3 DEGlist.tab

diff_genes <- read.delim(file = "../output/deseq/DEGlist.tab", sep =" ", header = TRUE)
diff_genes$access_num <- row.names(diff_genes) #adds the gene name into data frame as new column called gene
rownames(diff_genes) <- diff_genes$X #renames all the rows to 1-n instead of the gene name
diff_genes <- diff_genes[,c(7, 1:6)] #puts the gene column in front

---
title: "05-merge-blast-to-DEG-list"
author: "Sarah Tanja"
date: "`r format(Sys.time(), '%d %B, %Y')`"
format:
  html:
    df-print: paged
    toc: true
    toc-location: left
    smooth-scroll: true
    link-external-icon: true
    link-external-newwindow: true
    code-fold: false
    code-tools: true
    code-copy: true
    highlight-style: breeze
    code-overflow: wrap
    theme:
      light: flatly
      dark: darkly
---

```{r setup, include=FALSE}

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
)

```


### Install Packages

```{r install packages, filename='r'}
if ("tidyverse" %in% rownames(installed.packages()) == 'FALSE') install.packages('tidyverse')
if ("ggplot2" %in% rownames(installed.packages()) == 'FALSE') install.packages('ggplot2')
```


### Load Libraries

```{r load libraries, filename='r'}
library(tidyverse)
library(ggplot2)
```

### Merge the annotated table with the DEGlist

If you take a look at the DEGlist.tab, you will see that the row names themselves are the gene ID’s. This contrasts with the blast GO anotated table that has a whole column (V1) dedicated to the gene ID in the same format. Thus, we first need to take the row names of the DEGlist.tab and make them into a new column. It was originally in it’s own column but we needed to convert it so that it could go through the DESeq workflow.

```{r head DEGlist, engine='bash', filename='bash'}
cd ../output/deseq
head -n 3 DEGlist.tab
```

```{r, filename='r'}
diff_genes <- read.delim(file = "../output/deseq/DEGlist.tab", sep =" ", header = TRUE)
diff_genes$access_num <- row.names(diff_genes) #adds the gene name into data frame as new column called gene
rownames(diff_genes) <- diff_genes$X #renames all the rows to 1-n instead of the gene name
diff_genes <- diff_genes[,c(7, 1:6)] #puts the gene column in front
```