Generates gene-level summaries for each identified metabolic module.
The function exports tables containing module genes, positively scored
genes that were not selected into the final module, and the top correlated
genes from the complete expression dataset.
Each table includes gene identifiers, symbols, module scores, and
correlations with module expression patterns. These outputs provide a
detailed view of the transcriptional composition of every module.
Usage
getGeneTables(
modules,
nets,
patterns,
gene.exprs,
network.annotation,
work.dir = work.dir
)
Arguments
- modules
Metabolic modules.
- nets
Scored networks.
- patterns
Patterns of metabolic modules.
- gene.exprs
Gene expression.
- network.annotation
Metabolic network annotation.
- work.dir
Working directory where results should be saved.
Value
m.*.genes.tsv – module genes.
m.*.notInModule.genes.tsv – genes with positive score not included into module.
m.*.complete.genes.tsv – top 300 of all genes sorted by correlation value.
Results of this function can be seen in work.dir (three .tsv files for each module with gene lists).