Annotates metabolic modules using pathway enrichment analysis. For each module, over-representation analysis is performed against the pathway collection contained in the network annotation, followed by pathway redundancy reduction. The function exports pathway tables containing significantly enriched biological processes and their associated module genes. These annotations help connect discovered modules to known metabolic functions.
Usage
getAnnotationTables(
network.annotation,
nets,
work.dir,
pathways = NULL,
padj.threshold = Inf
)Arguments
- network.annotation
Metabolic network annotation.
- nets
Scored networks.
- work.dir
Working directory where files with module genes are (results will be saved here as well).
- pathways
Optional custom list of pathways for enrichment analysis. If NULL (default), pathways are taken from
network.annotation$pathways.- padj.threshold
Threshold, adjusted p-value, for pathways.