hypeR: Calculate enrichment of one or more signatures

In hypeR: An R Package For Geneset Enrichment Workflows

Description

Calculate enrichment of one or more signatures

Usage

hypeR(
  signature,
  genesets,
  test = c("hypergeometric", "kstest"),
  background = 23467,
  power = 1,
  absolute = FALSE,
  pval = 1,
  fdr = 1,
  plotting = FALSE,
  quiet = TRUE
)

Arguments

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

Value

A hyp object

Examples

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)

hypeR documentation built on Nov. 8, 2020, 8:19 p.m.