Package index • ultragsea

All functions

cor_pvalue(): Calculate p-value from correlation rho
cor_sparse_matrix(): Calculate sparse correlation matrix handling missing values
fgsea(): Fast replacement of fgsea with p/q values computed with ultragsea.cor
gmt2mat(): Convert GMT to Binary Matrix
goat(): Wrapper around GOAT
gset.cortest(): Calculate gene set correlation
gset.fastFET(): Calculate fast Fisher exact test.
gset.ztest(): Fast one sample z-test for matrix object F (e.g. foldchanges) and grouping matrix G (e.g. gene sets).
makeGseaResult(): Utility to convert fgsea/ultragsea style results to 'gseaResult' object compatible with clusterProfiler and enrichplot functions. Using this function you can use all plotting functions from enrichplot.
mat2gmt(): Convert Binary Matrix to GMT
matrix_metap(): Matrix version for combining p-values using fisher or stouffer method. Much faster than doing metap::sumlog() and metap::sumz()
phyper.fastFET(): Wrapper superfast version of Fisher Exact Test. This is the fastest implementation currently available. Uses phyper inside. Original code from 'corpora' R package
read.gmt(): Read GMT File
ultragsea(): Ultra-fast GSEA using z-score or geneset correlation. Results of these methods highly correlate with GSEA/fGSEA but are much faster.
write.gmt(): Write GMT File