runGSEA: Run gene-set enrichment analysis (GSEA)

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

Run gene-set enrichment analysis (GSEA)

Description

Run gene-set enrichment analysis (GSEA)

Usage

runGSEA(
  gene,
  value,
  species,
  db = "GO",
  my.entrez = NULL,
  my.pathway = NULL,
  min.size = 3,
  max.size = 300,
  do.plot = T,
  plot.top.n = 10,
  path.name.wrap.width = 40,
  e2s = F
)

Arguments

gene	Character vector of gene names
value	Numeric vector of values used to rank genes (e.g., logFC, expression, etc.). Must be same length as gene argument.
species	Species. One of "Mm" (mouse) or "Hs" (human)
my.entrez	Data.frame with SYMBOL and ENTREZID columns. Used to relate gene symbols to Entrez IDs. Retrieved internally unless explicitly provided.
my.pathway	Named list of pathways, with each entry containing vector of Entrez IDs. Retrieved internally unless explicitly provided.
min.size	Minimum gene set size. Default is 3.
max.size	Minimum gene set size. Default is 300.
do.plot	Logical to return dotplot visualizing top GSEA ranked pathways. Default is T.
plot.top.n	Numeric specifying how many top pathways to visualize. Default is 10.
path.name.wrap.width	Numeric specifying width of pathway names to wrap around. Argument passed to stringr::str_wrap(..., width = path.name.wrap.width)
e2s	entrez to symbol mapping (computationally demanding). Default False.

Value

list of enrichment results

Author(s)

Nicholas Mikolajewicz

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