brucemoran/cnormileglaucoma

What the Package Does (Title Case)

cnormileGlaucoma R package

This R package contains functions used to analyse the data contained in 'extdata'.

The PDF and XLSX files produced show significant pathways and the genes comprising them.

To install the repo: devtools::install_github("brucemoran/cnormileGlaucoma")

To run analyses: cnormileGlaucoma::run_analyses()

GSEA

The {msigdbr} package function msigdbr was used to with species = "Homo sapiens" and category = "H" to generate a pathway list object, msigdb_pathlist.

Data was read from XLSX files in the extdata directory. This data includes gene name and avg_log2FC columns. The {fgsea} function fgsea was run using pathways = msigdb_pathlist, stats = avg_log2FC as per the XLSX files which were sorted in decreasing rank as required, minSize = 15 and maxSize = 500. Results were sorted by descending normalised enrichment score (NES) value. For the group_markers_2024.xlsx analysis, cluster column was used to define the gene set and perform GSEA.

From these results, XLSX output was written for pathways with p-value < 0.05 for further interpretation. Plots per input XLSX were saved to PDF showing all analysed pathways, with indication of significant p-value pathways. The xlsx and pdf directories of the package hold these files. The ALL_HALLMARK_PATHWAYS.xlsx file in xlsx is the result of write_all_hallmarks(TAG, OUTDIR) function to write XLSX of Hallmark Pathways.