Perform_Pathway_Analysis_FGSEA: A Perform_Pathway_Analysis_FGSEA Function

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

A Perform_Pathway_Analysis_FGSEA Function

Description

This function allows you to perform differential gene analysis. Category: H, SubCategory: None Category: C2, SubCategory: CP=29, CP:KEGG=186, CP:PID=196, CP:BIOCARTA=292, CP:WIKIPATHWAYS=615, CP:REACTOME=1604, CGP=3368 Category: C5, SubCategory: GO:BP=7480, GO:CC=996, GO:MF=1707

Usage

Perform_Pathway_Analysis_FGSEA(
  Temp.object,
  saveDIR,
  SuffixName = "Pathway_FGSEA",
  msigdbrCategoryList = "H",
  SubmsigdbrCategorySubset = "",
  DownsamplePerIdent = "ALL",
  GroupName = "Cluster",
  minSizeGeneSet = 5,
  topnumber = 10,
  PDFheight = 10,
  PDFwidth = 12
)

Arguments

Temp.object	A list of Seurat objects between which to find anchors for downstream integration.
saveDIR	Path to save generated data.
SuffixName	Suffix. to be added in the directory name as
msigdbrCategoryList	Msigdb Category List. H, C1:C8. https://www.gsea-msigdb.org/gsea/msigdb/
SubmsigdbrCategorySubset	SubCategoryUse list based on MsigDB selected
DownsamplePerIdent	Number of cells to use per Idents
GroupName	Column to use for Identity
minSizeGeneSet	minimum Size of GeneSet for filtering
topnumber	Max #pathways to be plotted per group
PDFheight	PDFheight
PDFwidth	PDFwidth

Examples

Perform_Pathway_Analysis_FGSEA()

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