In most cases, it's more convenient to call the more generic test_genesets function which also deals with multiple-testing correction (per geneset source)
test_genesets_gsea(
genesets,
genelist,
score_type = NULL,
parallel_threads = 1L,
gseaParam = 1,
nPermSimple = 50000,
gsea_genelist_col = NULL,
gsea_scoretype = NULL,
random_seed = 123
)input genesets table with results in the "pvalue", "score_type" and "gsea_nes" columns
data.frame/tibble with geneset and gene columns
data.frame/tibble with gene and score columns. Should contain columns gene and either pvalue or effectsize, depending on score_type parameter
how to compute gene scores? options: "pvalue", "effectsize", "custom".
Option "pvalue" uses -log10 transformed values from the pvalue column in genelist.
Option "effectsize" uses values from the effectsize column in genelist as-is.
Option "custom" expects 2 additional parameters; gsea_genelist_col should be a column name in genelist to be used for fGSEA (values used as-is), gsea_scoretype should be the respective value for the fGSEA scoreType parameter ('pos', 'neg' or 'std)
number of threads to use for parallel processing. Set to 0 to automatically select all available processors/cores, set to 1 to disable (default) or to N to use N processes. Note that multiprocessing sometimes breaks on RStudio + Windows, hence this parameter is set to 1 to disable multiprocessing by default for now
passed to fgsea::fgsea(), from manual: "GSEA parameter value, all gene-level statis are raised to the power of 'gseaParam' before calculation of GSEA enrichment scores.". default = 1. Further comments by fGSEA author at https://github.com/ctlab/fgsea/issues/45
passed to fgsea::fgsea(), from manual: "Number of permutations in the simple fgsea implementation for preliminary estimation of P-values.". default = 50000 in this R package but 1000 by default in fGSEA v1.22.0; we observed much better accuracy in null simulations when increasing this from default 1k to 10k and further minor improvement towards 50k, hence the latter is our default
optional, only used for score_type "custom"
optional, only used for score_type "custom"
the random seed that is passed to set.seed() in order to ensure fgsea results are reproducible. default: 123
test_genesets