Identify correlated genes/pathways associated with differential abundance.

da_DEG(
  da.res.list,
  reduction = "pca",
  species = "Mm",
  red.gene.percentile = 0.99,
  do.enrich = F,
  pathway.db = "Bader"
)

Arguments

da.res.list: da_Run output.
reduction: Character specifying which reduction to use for differential abundance association analysis.
species: Character specifying species. Either "Mm" or "Hs". Default is "Mm".
red.gene.percentile: Numeric, top nth percentile genes/pathways.
do.enrich: Logical to perform enrichment of DA-associated genesets.
pathway.db: Character pathway database to use for enrichment. Ignored if do.enrich = F. Default: "Bader".

updated da_Run output.

Nicholas Mikolajewicz