generic function for gene set enrichment analysis
gsea_gson(
geneList,
gson,
nPerm = 1000,
exponent = 1,
minGSSize = 10,
maxGSSize = 500,
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
method = "multilevel",
adaptive = FALSE,
minPerm = 101,
maxPerm = 1e+05,
pvalThreshold = 0.1,
verbose = TRUE,
...
)gseaResult object
A named numeric vector of gene statistics (e.g., log fold change), ranked in descending order.
A GSON object containing gene set information.
Number of permutations for p-value calculation (default: 1000).
Weighting exponent for enrichment score (default: 1.0).
minimal size of each geneSet for analyzing
maximal size of each geneSet for analyzing
P-value cutoff.
P-value adjustment method (e.g., "BH").
Permutation method.
Logical. Use adaptive permutation.
Minimum permutations for adaptive mode.
Maximum permutations for adaptive mode.
P-value threshold for early stopping.
Logical. Print progress messages.
Additional parameters passed to gsea()
Guangchuang Yu