01_Lab_data_integration.Rmd

---
title: "NOVA_Lab_Exp"
author: "Natalia Andrade"
date: "2022-12-09"
output:
  pdf_document: default
  html_document: default
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r}
library(ggplot2)
library(tidyr)
library(dplyr)
library(stringr)
library(reshape2)
```
#Bind lab data of each time point together
```{r}
TP1<- read.csv("raw_data/TP1_data.csv")
TP1$RNA_Original_concentration<- as.integer(TP1$RNA_Original_concentration)
TP1$Cq<- as.character(TP1$Cq)
# 12 samples were extracted in Plate 8

TP2<- read.csv("raw_data/TP2_data.csv")
TP2$Cq<- as.character(TP2$Cq)

TP3<- read.csv("raw_data/TP3_data.csv")
TP3$Cq<- as.character(TP3$Cq)

names(TP1)
names(TP2)
names(TP3)


NOVA_lab<- bind_rows(TP1, TP2, TP3) 

#write.csv(NOVA_lab, "raw_data/NOVA_lab.csv")
```


##### ### Integrating Metadata and Lab data ###
```{r}
meta_NOVA<- read.csv("raw_data/metadata_final_long.csv")

names(meta_NOVA)

meta_NOVA_lab<- meta_NOVA %>% 
  
                mutate(Sample_ID = paste(Falcon_Tube, ID,sep = "_")) %>% 
  
                mutate(Sample_name = paste(Sample_Period, ID,sep = "_")) %>% 
                
              full_join(NOVA_lab, by="Sample_ID") 


write.csv(meta_NOVA_lab,"data/meta_NOVA_lab.csv")
```