hypeR {hypeR} | R Documentation |
Perform hyper enrichment
hypeR(signature, gsets, test = c("hypergeometric", "kstest"), bg = 23467, pval_cutoff = 1, fdr_cutoff = 1, weights_pwr = 1, absolute = FALSE, do_plots = FALSE, verbose = FALSE)
signature |
A vector of symbols |
gsets |
A list of genesets or a relational genesets object |
test |
Choose an enrichment type e.g. c("hypergeometric", "kstest") |
bg |
Size or character vector of background population genes |
pval_cutoff |
Filter results to be less than pval cutoff |
fdr_cutoff |
Filter results to be less than fdr cutoff |
weights_pwr |
Exponent for weights (Subramanian et al.) |
absolute |
Takes max-min score rather than the max deviation from null |
do_plots |
Use true to generate plots |
verbose |
Use false to suppress logs |
A hyp object
gsets <- hyperdb_fetch(type="gsets", "KEGG_2019_Human") signature <- c("IDH3B","DLST","PCK2","CS","PDHB","PCK1","PDHA1","LOC642502", "PDHA2","LOC283398","FH","SDHD","OGDH","SDHB","IDH3A","SDHC", "IDH2","IDH1","OGDHL","PC","SDHA","SUCLG1","SUCLA2","SUCLG2") # Perform hyper enrichment hyp_obj <- hypeR(signature, gsets, bg=2522, fdr_cutoff=0.05)