---
title: "Untitled"
output: html_document
date: "2025-02-26"
---

```{r}
library(tidyverse)
```


```{r}
### This is the merged rnaseq counts for the 5 projects
data <- read.delim2("C:/Users/EmmaStrand/MyProjects/Resilience_Biomarkers_Aquaculture/Cvirg_Pmarinus_RNAseq/data/rnaseq_gene_counts/merged_gene_counts.tsv")

genes <- data %>% dplyr::select(gene_id) %>% distinct()
### 38,828 genes from merged set 

### length example
dataset1_lengths <- read.delim2("C:/Users/EmmaStrand/MyProjects/Resilience_Biomarkers_Aquaculture/Cvirg_Pmarinus_RNAseq/data/rnaseq_gene_lengths/salmon.merged.gene_lengths_dataset1.tsv")

######## decided on the length scaled counts 
dataset1_scaled <- read.delim2("C:/Users/EmmaStrand/MyProjects/Resilience_Biomarkers_Aquaculture/Cvirg_Pmarinus_RNAseq/data/rnaseq_gene_counts/salmon.merged.gene_counts_length_scaled_dataset1.tsv")
dataset2_scaled <- read.delim2("C:/Users/EmmaStrand/MyProjects/Resilience_Biomarkers_Aquaculture/Cvirg_Pmarinus_RNAseq/data/rnaseq_gene_counts/salmon.merged.gene_counts_length_scaled_dataset2.tsv")
dataset3_scaled <- read.delim2("C:/Users/EmmaStrand/MyProjects/Resilience_Biomarkers_Aquaculture/Cvirg_Pmarinus_RNAseq/data/rnaseq_gene_counts/salmon.merged.gene_counts_length_scaled_dataset3.tsv")
dataset4_scaled <- read.delim2("C:/Users/EmmaStrand/MyProjects/Resilience_Biomarkers_Aquaculture/Cvirg_Pmarinus_RNAseq/data/rnaseq_gene_counts/salmon.merged.gene_counts_length_scaled_dataset4.tsv")
dataset5_scaled <- read.delim2("C:/Users/EmmaStrand/MyProjects/Resilience_Biomarkers_Aquaculture/Cvirg_Pmarinus_RNAseq/data/rnaseq_gene_counts/salmon.merged.gene_counts_length_scaled_dataset5.tsv")

dataset_scaled_joined <- full_join(dataset1_scaled, dataset2_scaled) %>% full_join(., dataset3_scaled) %>%
  full_join(., dataset4_scaled) %>% full_join(., dataset5_scaled)

length(unique(dataset_scaled_joined$gene_id)) ## 38,828
ncol(dataset_scaled_joined) - 2 ## number of samples = 217

dataset_scaled_joined %>% 
  write_delim("C:/Users/EmmaStrand/MyProjects/Resilience_Biomarkers_Aquaculture/Cvirg_Pmarinus_RNAseq/data/rnaseq_gene_counts/merged_gene_counts_scaled.tsv")
```