da_DEG: Identify correlated genes/pathways associated with...

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Identify correlated genes/pathways associated with differential abundance.

Description

Identify correlated genes/pathways associated with differential abundance.

Usage

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".

Value

updated da_Run output.

Author(s)

Nicholas Mikolajewicz

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.