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()
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.