001_Directories.Rmd

---
title: "CAMDA2024 - Microbiom"
subtitle: "001_Directories"
author: "David Alberto García Estrada"
date: "`r Sys.Date()`"
output: html_document
---

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

# Directories

## Main Working Directory 

We adjust the working area

```{r}
# Display current directory
getwd()
# If necessary, change the path where the stored files are located. 
workingDir <- "."
setwd(workingDir)
```

## Other directories

Data and Results

```{r}
Data <- "Data/"
dir.create(Data, showWarnings = FALSE)
Results <- "Results/"
dir.create(Results, showWarnings = FALSE)

TypeData <- c("Gut", "Covid", "Kraken", "Braken")
SubResults <- c("Abundance", "Diversity", 
                "DifferentialTaxa", "DifferentialFunction", 
                "VennDiagramTaxa", "VennDiagramFunction")

for (data in TypeData){
  # Data
  D.dir <- paste0(Data, data, "/")
  dir.create(D.dir, showWarnings = FALSE)
  # Results
  R.dir <- paste0(Results, data, "/")
  dir.create(R.dir, showWarnings = FALSE)
  
  # SubResults
  for (subres in SubResults){
    SR.dir <- paste0(R.dir, subres, "/")
    dir.create(SR.dir, showWarnings = FALSE)
  }
}
```