hypeR {hypeR}R Documentation

Perform hyper enrichment

Description

Perform hyper enrichment

Usage

hypeR(symbols, gsets, bg = 23467, min.drawsize = 4, pval.cutoff = 1,
  fdr.cutoff = 1, verbose = FALSE)

Arguments

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

Value

A hyper dataframe

Examples

# 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)


[Package hypeR version 1.00.0 Index]