Perform_GeneOntology_Analysis_Using_Marker_Genes: A Perform_GeneOntology_Analysis_Using_Marker_Genes Function...

In parveendabas/SCA: What the Package Does (One Line, Title Case)

A Perform_GeneOntology_Analysis_Using_Marker_Genes Function Except EnrichR, all others uses DEGs

Description

This function allows you to perform differential gene analysis.

Usage

Perform_GeneOntology_Analysis_Using_Marker_Genes(
  Temp.object,
  Temp.MarkerList,
  saveDIR,
  SuffixName = "GO",
  methods = c("ClusterProfilerM", "ClusterProfilerAlt1", "ClusterProfilerAlt2"),
  EnrichDB = "GO_Biological_Process_2021",
  GroupNameDEGs = "cluster",
  OrgDB = org.Mm.eg.db,
  OrgName = "mmu",
  topnumber = 10,
  PDFheight = 12,
  PDFwidth = 18
)

Arguments

Temp.object	A list of Seurat objects between which to find anchors for downstream integration.
Temp.MarkerList	A data.frame containg marker genes.
saveDIR	Path to save generated data.
SuffixName	Suffix. to be added in the directory name as
methods	ClusterProfiler (enrichGO)
EnrichDB	EnrichR DB. For list of DBs: listEnrichrDbs()... https://maayanlab.cloud/Enrichr/#libraries
GroupNameDEGs	ClusterProfiler (enrichGO)
OrgDB	ClusterProfiler (enrichGO)
OrgName	ClusterProfiler (enrichGO)
topnumber	Max #pathways to be plotted per group
PDFheight	PDFheight
PDFwidth	PDFwidth

Examples

Perform_GeneOntology_Analysis_Using_Marker_Genes()

parveendabas/SCA documentation built on Sept. 19, 2022, 8:31 a.m.