ThresholdSets: Return a vector of genes that pass a threshold for includions

In dgrtwo/GSEAMA: Gene set enrichment analysis made awesome

Description

Return a vector of genes that pass a threshold of "significance" or other kind of inclusion. For tests with a p-value (t-test, Wilcoxon, hypergeometric), this is FDR-controlled p-values. For LASSO, this is all cases where beta1sd != 0.

Usage

ThresholdSets(m, alpha = 0.05, method = "fdr", ...)

Arguments

m	GeneMatrix object
alpha	Threshold for (corrected) p-values, not used in LASSO
method	Method, passed to p.adjust, or "qvalue" to use qvalue. Not used in LASSO
...	Extra arguments to pass on to correction method

See Also

p.adjust, p.adjust.methods

dgrtwo/GSEAMA documentation built on May 15, 2019, 7:22 a.m.