hypeR {hypeR} | R Documentation |
Calculate enrichment of one or more signatures
hypeR( signature, genesets, test = c("hypergeometric", "kstest"), background = 23467, power = 1, absolute = FALSE, pval = 1, fdr = 1, plotting = FALSE, quiet = TRUE )
signature |
A vector of symbols |
genesets |
A gsets/rgsets object or a named list of genesets |
test |
Choose an enrichment type e.g. c("hypergeometric", "kstest") |
background |
Size or character vector of background population genes |
power |
Exponent for weights (kstest only) |
absolute |
Takes max-min score rather than the max deviation from null (kstest only) |
pval |
Filter results to be less than pval cutoff |
fdr |
Filter results to be less than fdr cutoff |
plotting |
Use true to generate plots for each geneset test (may slow performance) |
quiet |
Use true to suppress logs and warnings |
A hyp object
genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG") 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") hyp_obj <- hypeR(signature, genesets, background=2522)