Repository for all R scripts and results involved in my final year research project for the Biomedical Health and Life Sciences degree in University College Dublin.
Project title - "Bioinformatic Analysis of Copy Number Alteration Signature Mechanisms in Ovarian Carcinoma".
There were four method components involved in this project:
- Confirming copy number alteration (CNA) signature findings from a previously published high grade serous ovarian cancer (HGSOC) study (Macintyre et al 2018 - "Copy number signatures and mutational processes in ovarian carcinoma").
- Differential gene expression profiling for the CNA signatures identified in 1.
- RNA signature identification using the results of 2.
- Survival analysis of CNA and RNA signature classifications.
Scripts for part 1: "Signatures" folder
signature_extrapolation - CNA signature extrapolation for TCGA HGSOC data, as performed by Macintyre et al 2018. All_Sig_Functions - all functions required for signature extrapolation and formatting of CNA signature results for downstream analysis.
Scripts for parts 2, 3 and 4: "Post_signature_analysis" folder
DE_RNA_survival - differential gene expression profiling, RNA signature identification and survival analysis. Post_sig_functions - all extra functions required for the DE_RNA_survival script.
All main output results are located in the "Results" folder.
sessionInfo for parts 1 and 2-4 can also be viewed.
Due to file size limitations (25MB), full DE results could not be uploaded to GitHub but can be shared upon request.