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01_structure.Rmd
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---
title: "Structure"
author: "Sudarshan"
date: "14 augustus 2019"
output: html_document
---
Data generated include:
Three main data were generated.
1. Wetlab (optical density, pH, HPLC, GC)
2. Amplicon (16S rRNA gene V5-V6 region)
3. Metatranscriptomics (mRNA sequecing)
```{r}
dir.create("01_exploratory")
dir.create("01_exploratory/data")
dir.create("01_exploratory/output")
dir.create("01_exploratory/output/rds")
dir.create("01_exploratory/output/figs")
dir.create("01_exploratory/output/tables")
```
```{r}
dir.create("02_wetlab")
dir.create("02_wetlab/data")
dir.create("02_wetlab/output")
dir.create("02_wetlab/output/rds")
dir.create("02_wetlab/output/figs")
dir.create("02_wetlab/output/tables")
```
```{r}
dir.create("03_amplicon")
dir.create("03_amplicon/data")
dir.create("03_amplicon/codes")
dir.create("03_amplicon/output")
dir.create("03_amplicon/output/rds")
dir.create("03_amplicon/output/figs")
dir.create("03_amplicon/output/tables")
```
```{r}
dir.create("04_metatrans")
dir.create("04_metatrans/data")
dir.create("04_metatrans/output")
dir.create("04_metatrans/output/rds")
dir.create("04_metatrans/output/figs")
dir.create("04_metatrans/output/tables")
```
## Metatranscriptomics
This section has several subsections.
I will define KEGG based anlaysis as one main section with subsections for pathway analysis, gut metabolic modules analysis, etc.
```{r}
# I will define KEGG based anlaysis as one main section with subsections for pathway analysis, gut metabolic modules analysis, etc.
dir.create("04_metatrans/05_kegg_analysis")
dir.create("04_metatrans/05_kegg_analysis/kegg_brite")
dir.create("04_metatrans/05_kegg_analysis/codes")
dir.create("04_metatrans/05_kegg_analysis/data")
dir.create("04_metatrans/05_kegg_analysis/tables")
dir.create("04_metatrans/05_kegg_analysis/figs")
dir.create("04_metatrans/05_kegg_analysis/rds")
dir.create("04_metatrans/05_kegg_analysis/01_output")
dir.create("04_metatrans/05_kegg_analysis/02_pathway_anlaysis")
dir.create("04_metatrans/05_kegg_analysis/02_pathway_anlaysis/tables")
dir.create("04_metatrans/05_kegg_analysis/02_pathway_anlaysis/figs")
dir.create("04_metatrans/05_kegg_analysis/03_gmm_anlaysis")
dir.create("04_metatrans/05_kegg_analysis/03_gmm_anlaysis/figs")
dir.create("04_metatrans/05_kegg_analysis/03_gmm_anlaysis/tables")
dir.create("04_metatrans/05_kegg_analysis/03_gmm_anlaysis/data")
dir.create("04_metatrans/05_kegg_analysis/04_reveco_anlaysis")
dir.create("04_metatrans/05_kegg_analysis/04_reveco_anlaysis/data")
dir.create("04_metatrans/05_kegg_analysis/04_reveco_anlaysis/output")
dir.create("04_metatrans/05_kegg_analysis/04_reveco_anlaysis/output/rds")
dir.create("04_metatrans/05_kegg_analysis/04_reveco_anlaysis/output/tables")
dir.create("04_metatrans/05_kegg_analysis/04_reveco_anlaysis/output/figs")
dir.create("04_metatrans/06_species_composition")
#dir.create("04_metatrans/06_species_composition")
dir.create("04_metatrans/06_species_composition/output")
```