Description Usage Arguments Value Examples
Calculate enrichment of one or more signatures
1 2 3 4 5 6 7 8 9 10 11 12 |
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
1 2 3 4 5 6 7 | 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)
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