Data Source

The data is sourced from TCGA, specifically the BRCA cohort, using the curatedTCGAData R package.

Analysis

• Downloading TCGA Data: The analysis begins with downloading multiomic data (RNASeq, Mutation, Methylation) for the BRCA cohort using curatedTCGAData.
• Sample Mapping and Clinical Data Analysis: Processing sample mapping and clinical data, including creating factors for pathology stages and examining relationships between tumor stage and vital status.
• Mutation Data Analysis: Accessing and processing mutation data, analyzing mutation prevalence, and ensuring consistency with clinical data.
• RNA-Seq Data Analysis: Analyzing gene expression levels and examining the relationship between gene expression and clinical features.
• Methylation Data Analysis: Processing methylation data and preparing for correlation analysis.
• Correlation Analysis: Calculating correlations between methylation and RNA-Seq data for specific genes.
• Visualization: Creating visualizations for mutation frequencies, gene expressions, and methylation patterns.

Getting Started

1. Clone the repository.
2. Install required R packages.
3. Run the Rmd notebooks to replicate the analysis.

Dependencies

• R version 4.3.1

Refer to requirements.txt for a full list of required R packages.

Author

Tarsus Lam