hypeR {hypeR} | R Documentation |
Perform hyper enrichment
hypeR(symbols, gsets, bg = 23467, min.drawsize = 4, pval.cutoff = 1, fdr.cutoff = 1, verbose = FALSE)
symbols |
A character vector of gene symbols |
gsets |
A list of gene sets |
bg |
Size or character vector of background population genes |
min.drawsize |
Min number of drawn items that must be among categories items |
pval.cutoff |
Filter results to be less than pval cutoff |
fdr.cutoff |
Filter results to be less than fdr cutoff |
verbose |
Use false to suppress logs |
A hyper dataframe
# Grab a list of curated gene sets REACTOME <- ex_get("C2.CP.REACTOME") # Genes involed in tricarboxylic acid cycle symbols <- 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 <- hypeR(symbols, REACTOME, bg=2522, fdr=0.05)