iterative.bulk.gsea {liger} | R Documentation |
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 |
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
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)
[Package liger version 2.0.1 Index]