R Code For 4 Datasets (FC/FDR)
Number of Functions: 5 functions have been written.
1. DownloadGEO()
Purpose: Downloads a GEO dataset, extracts the expression matrix, phenotype data, and annotation, and saves them to files.
Key Steps:
- Downloads the dataset.
- Performs log2 transformation if necessary.
- Saves matrix, phenotype, and annotation data to CSV/TSV files.
2. DEGanalysis()
Purpose: Performs differential expression analysis using limma.
Key Steps:
- Loads matrix and phenotype files.
- Groups samples by subtype or grade.
- Fits a linear model and creates a top table of DEGs.
- Saves the DEGs and associated annotation data.
3. Makevolcano()
Purpose: Generates volcano plots to visualize DEGs.
Key Steps:
- Reads DEGs from TSV.
- Categorizes genes into upregulated, downregulated, or non-significant.
- Creates interactive volcano plots using plotly or ggplot2.
4. Makenetworkanalyst()
Purpose: Prepares files for network analysis based on the results of differential expression analysis.
Key Steps:
- Extracts up/down-regulated genes and formats the data for network analysis.
- Saves the results for further analysis.
5. MakeVenna()
Purpose: Creates a Venn diagram to visualize common differentially expressed genes across multiple datasets.
Key Steps:
- Identifies common genes among datasets.
- Generates a Venn diagram using ggvenn.
Packages Used:
- GEOquery: For downloading and processing GEO datasets.
- limma: For performing differential expression analysis.
- tidyverse: For data manipulation and visualization.
- plotly & ggplot2: For interactive and static plots.
- ggvenn: For creating Venn diagrams.