mod_gsea {CEMiTool} | R Documentation |
Perfoms Gene Set Enrichment Analysis (GSEA) for each co-expression module found.
mod_gsea(cem, ...) ## S4 method for signature 'CEMiTool' mod_gsea(cem, gsea_scale = TRUE, rank_method = "mean", gsea_min_size = 15, gsea_max_size = 500, verbose = FALSE)
cem |
Object of class |
... |
Optional parameters. |
gsea_scale |
If TRUE, transform data using z-score transformation. Default: TRUE |
rank_method |
Character string indicating how to rank genes. Either "mean" (the default) or "median". |
gsea_min_size |
Minimum gene set size |
gsea_max_size |
Maximum gene set size |
verbose |
logical. Report analysis steps. |
GSEA results.
# Get example CEMiTool object data(cem) # Look at example annotation file sample_annotation(cem) # Run GSEA on network modules cem <- mod_gsea(cem) # Check results gsea_data(cem)