Run gene-set enrichment analysis (GSEA)

Run gene-set enrichment analysis (GSEA)

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

Nicholas Mikolajewicz