BIGsea: BIGsea

In basilinb/SEARchways: One place for GSEA, enrichr and clusterprofiler

BIGsea

Description

Run GSEA on multiple list using fgsea. More information about GSEA and geneset databases check https://www.gsea-msigdb.org/gsea/msigdb

Usage

BIGsea(
  gene_list,
  gmt_ls = NULL,
  nperm = 1000,
  group = NULL,
  subgroup = NULL,
  S = "human"
)

Arguments

gene_list	named list object with named numeric vectors of gene symbols and logFC
gmt_ls	list object with gene ontology data
nperm	number of permutations for P-value calculations. Default is 1000
group	Which Geneset database you want to run GSEA on
subgroup	Specify subgroup of Geneset database you want to run GSEA on. Below is the list of commonly used Genesets Group Sub-group C1 C2 CGP C2 CP C2 CP:BIOCARTA C2 CP:KEGG C2 CP:PID C2 CP:REACTOME C2 CP:WIKIPATHWAYS C3 C5 GO:BP C5 GO:CC C5 GO:MF C5 HPO C6 H
S	Specify specie for Geneset database default is human

Value

Output of a list of list with GSEA results

basilinb/SEARchways documentation built on March 29, 2022, 12:04 a.m.