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 1.3.0 Index]