Native implementation of GSEA

Usage

gsea_sample_perm(
  expr,
  condition,
  gs,
  direction = c("std", "pos", "neg"),
  power = 1,
  min_size = 5,
  max_size = 1000,
  nperm = 1000,
  verbose = TRUE
)

gsea_gene_perm(
  s,
  gs,
  direction = c("std", "pos", "neg"),
  power = 1,
  min_size = 5,
  max_size = 1000,
  nperm = 1000,
  verbose = TRUE
)

Arguments

expr: The complete expression matrix.
condition: The condition labels of samples. The value should be a factor where level[1] corresponds to the treatment group and level[2] corresponds to the control group.
gs: A list of gene sets. Genes should have the same ID types as expr.
direction: Whether the test is one-sided or two-sided.
power: Power added to the absolute value of weight.
min_size: Minimal size of gene sets for analysis.
max_size: Maximal size of gene sets for analysis.
nperm: Number of permutations.
verbose: Whether to print messages?
s: A numeric vector of gene scores.

Details

The two functions are only for the purpose of studying.