liger (version 2.0.1)

iterative.bulk.gsea: Iterative bulk gene set enrichment analysis

Description

Iterative bulk gene set enrichment analysis

Usage

iterative.bulk.gsea(
  ...,
  set.list,
  threshold.eval = 10,
  n.rand = c(100, 1000, 10000),
  verbose = TRUE
)

Arguments

...

arguments to be passed to bulk.gsea

set.list

list of gene sets

threshold.eval

threshold for applying additional permutations (default: 10)

n.rand

list of number of random permutations used to assess significance (default: c(1e2,1e3,1e4))

verbose

whether to use high verbosity level (default: TRUE)

Examples

# NOT RUN {
data("org.Hs.GO2Symbol.list")  
universe <- unique(unlist(org.Hs.GO2Symbol.list))  # get universe
gs <- org.Hs.GO2Symbol.list[[1]]  # get a gene set
vals <- rnorm(length(universe), 0, 10)  # simulate values
names(vals) <- universe
vals[gs] <- rnorm(length(gs), 100, 10)  
gs.list <- org.Hs.GO2Symbol.list # get gene sets
# reduce n.rand for speed
iterative.bulk.gsea(values = vals, set.list = gs.list[1:3], mc.cores = 1, n.rand=100) 

# }