hypeR: Calculate enrichment of one or more signatures

Description Usage Arguments Value Examples

View source: R/hype.R

Description

Calculate enrichment of one or more signatures

Usage

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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

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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.