This function performs pathway enrichment analysis. Uses the DOSE package with the internal function enricher_internal.
Usage
pathway_enrich(
gene,
organism = "ppu",
keyType = "kegg",
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
universe,
minGSSize = 10,
maxGSSize = 500,
qvalueCutoff = 0.2,
use_internal_kegg = FALSE,
custom_gene_sets = FALSE,
custom_pathways = NULL
)Arguments
- gene
A numeric vector or a character vector of gene symbols that were found enriched in a differential expression analysis.
- organism
A character string. The organism to use. Default is "ppu" for Pseudomonas putida KT2440.
- keyType
A character string. The type of gene ID. Default is "kegg".
- pvalueCutoff
A numeric value. The cutoff of p-value. Default is 0.05.
- pAdjustMethod
A character string. The method of p-value adjustment. Default is "BH".
- universe
A numeric vector or a character vector of gene symbols.
- minGSSize
A numeric value. The minimum gene set size. Default is 10.
- maxGSSize
A numeric value. The maximum gene set size. Default is 500.
- qvalueCutoff
A numeric value. The cutoff of q-value. Default is 0.2.
- use_internal_kegg
A logical value. Whether to use internal KEGG database. Default is FALSE.
- custom_gene_sets
A logical value. Whether to use custom gene sets. Default is FALSE.
- custom_pathways
A data frame. The custom pathways to use. Needs to have column "Pathway" and corresponding "Accession" column with comma-separated entries of gene/protein identifiers for that pathway.