pathwayenrichment-methods: Pathway enrichment analysis

In edroaldo/fusca: Framework for Unified Single-Cell Analysis

Pathway enrichment analysis

Description

Pathway enrichment analysis on genes up or down-regulated along trajectories.

Usage

pathwayenrichment(
  object,
  names,
  cc = NULL,
  species = c("Hs", "Mm"),
  annotation,
  ids
)

## S4 method for signature 'CellRouter'
pathwayenrichment(
  object,
  names,
  cc = NULL,
  species = c("Hs", "Mm"),
  annotation,
  ids
)

Arguments

object	CellRouter object.
names	character vector; selected trajectories.
cc	character vector; list of cell cycle genes or other gene lists to be removed from the genes up or down-regulated in each trajectory.
species	character; species: Hs for Homo Sapiens or Mm for Mus Musculus.
annotation	character; organism-specific annotations: 'mouse' or 'org.Mm.eg.db', or 'human' or 'org.Hs.eg.db'.
ids	table containing mappings between gene identifiers.

Value

CellRouter object with the pathwayenrichment slot updated.

edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.