hypeR {hypeR}R Documentation

Perform hyper enrichment

Description

Perform hyper enrichment

Usage

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)

Arguments

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

Value

A hyp object

Examples

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)


[Package hypeR version 1.2.0 Index]