Performs pathway enrichment analysis using either Over-representation Analysis (ORA) or Gene Set Enrichment Analysis (FGSEA) based on the provided gene set and pathways.
Usage
pathwayAnalysis(
gene_set,
pathways,
method = "ORA",
species = "Homo sapiens",
id_col = "gene_symbol",
pcutoff = 0.05,
verbose = TRUE
)Arguments
- gene_set
A data frame containing the differential expression results. Rows represent genes.
- pathways
A data frame containing pathway information, with columns for pathways and associated genes.
- method
A string specifying the pathway analysis method. Options are `"ORA"` for Over-representation Analysis or `"FGSEA"` for Gene Set Enrichment Analysis. Default is `"ORA"`.
- species
A string specifying the species for which the pathways are relevant. Default is `"Homo sapiens"`.
- id_col
A string specifying the column in the `pathways` data frame that contains gene identifiers. Default is `"gene_symbol"`.
- pcutoff
A numeric value specifying the adjusted p-value cutoff for significant pathways. Default is `0.05`.
- verbose
A logical value indicating whether to display progress messages. Default is `TRUE`.
Value
A data frame containing pathway enrichment results, including pathway names, p-values, adjusted p-values, and other relevant statistics.
Details
This function allows users to perform pathway enrichment analysis using either ORA or FGSEA. The `pathways` input should include a column specifying gene identifiers and a column specifying pathway names.
- **ORA**: Identifies pathways over-represented in the provided gene set. - **FGSEA**: Identifies pathways using a ranked list of genes based on differential expression statistics.
The function dynamically calls internal implementations of ORA or FGSEA based on the `method` argument.